nixpkgs mirror (for testing) github.com/NixOS/nixpkgs
nix
at python-updates 17692 lines 837 kB view raw
1{ 2 "extraArgs": { 3 "biocVersion": "3.22" 4 }, 5 "packages": { 6 "ABSSeq": { 7 "name": "ABSSeq", 8 "version": "1.64.0", 9 "sha256": "0cvq7n71i784agdyl2l4fxmla5sd04nqb6z35pc8k0lqh6319bh4", 10 "depends": ["limma", "locfit"] 11 }, 12 "ABarray": { 13 "name": "ABarray", 14 "version": "1.78.0", 15 "sha256": "0y8hf8ziyh4v5q47ysbrld402z4vwd5dgkh21fvrq13r99vx4fpx", 16 "depends": ["Biobase", "multtest"] 17 }, 18 "ACE": { 19 "name": "ACE", 20 "version": "1.28.0", 21 "sha256": "09bcqwkxswn8zxnp66xbqv8p71z8fdnipr1v1cfn4m64q9jjjir5", 22 "depends": ["Biobase", "GenomicRanges", "QDNAseq", "ggplot2"] 23 }, 24 "ACME": { 25 "name": "ACME", 26 "version": "2.66.0", 27 "sha256": "0fklsn5clzni4fsnipgkkikbr09fiwlkrsf3gqnyzl1kwwlwxiy2", 28 "depends": ["Biobase", "BiocGenerics"] 29 }, 30 "ADAM": { 31 "name": "ADAM", 32 "version": "1.26.0", 33 "sha256": "12s2dlfnkg13jgh8dppcjk5sfhw88c63iqzmf9c4sb5q9i2ydy8x", 34 "depends": ["DT", "GO_db", "KEGGREST", "Rcpp", "SummarizedExperiment", "dplyr", "knitr", "pbapply", "stringr"] 35 }, 36 "ADAMgui": { 37 "name": "ADAMgui", 38 "version": "1.26.0", 39 "sha256": "1gn460fdbcdngzjq4llyq08fzgaqds6msvya8967cz5c6cg70f7j", 40 "depends": ["ADAM", "DT", "GO_db", "RColorBrewer", "colorRamps", "data_table", "dplyr", "ggplot2", "ggpubr", "ggrepel", "ggsignif", "gridExtra", "knitr", "reshape2", "shiny", "shinyjs", "stringi", "stringr", "testthat", "varhandle"] 41 }, 42 "ADAPT": { 43 "name": "ADAPT", 44 "version": "1.4.0", 45 "sha256": "1v0lypbv1bhxphd071rn3b8kyvfn088nx78fg3kadlgc0y5xvli5", 46 "depends": ["Rcpp", "RcppArmadillo", "RcppParallel", "ggplot2", "ggrepel", "phyloseq"] 47 }, 48 "ADImpute": { 49 "name": "ADImpute", 50 "version": "1.20.0", 51 "sha256": "1dnw40hnrjyd3bbb1ylw0fy8lcc6irswd80px69p8c7kmwp2yfp1", 52 "depends": ["BiocParallel", "DrImpute", "MASS", "Matrix", "S4Vectors", "SAVER", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "data_table", "kernlab", "rsvd"] 53 }, 54 "ADaCGH2": { 55 "name": "ADaCGH2", 56 "version": "2.50.0", 57 "sha256": "12p0fffq1aa8mnibjwg10b7f4bhr9brg6jniz9amzr5hink5xvy6", 58 "depends": ["DNAcopy", "aCGH", "bit", "cluster", "ff", "tilingArray", "waveslim"] 59 }, 60 "AGDEX": { 61 "name": "AGDEX", 62 "version": "1.58.0", 63 "sha256": "0xwlm7nay7ns5nnvi6zrl2ygrbkj6lq14yph6rasy08cdjll74l2", 64 "depends": ["Biobase", "GSEABase"] 65 }, 66 "AHMassBank": { 67 "name": "AHMassBank", 68 "version": "1.10.0", 69 "sha256": "1kx70njam0b05ind94r55dm99a5b2x01akipvz7q9bhqrcl0qbq7", 70 "depends": ["AnnotationHubData"] 71 }, 72 "AIMS": { 73 "name": "AIMS", 74 "version": "1.42.0", 75 "sha256": "0y0shffhx5axm14m0wwns7x2aydzwhwd1x28an2c3y34x03bp98x", 76 "depends": ["Biobase", "e1071"] 77 }, 78 "ALDEx2": { 79 "name": "ALDEx2", 80 "version": "1.42.0", 81 "sha256": "0ajpmb60yyc6z6w8vjy6anxla4cih6229a5d8q0g279s2pg6s8lr", 82 "depends": ["BiocParallel", "GenomicRanges", "IRanges", "Rfast", "S4Vectors", "SummarizedExperiment", "directlabels", "lattice", "latticeExtra", "multtest", "zCompositions"] 83 }, 84 "AMARETTO": { 85 "name": "AMARETTO", 86 "version": "1.26.0", 87 "sha256": "1ynzmipszc22d1zcw4w4lslcvdappw12c1csckqz94bibfgngjmq", 88 "depends": ["BiocFileCache", "ComplexHeatmap", "DT", "Matrix", "MultiAssayExperiment", "Rcpp", "callr", "circlize", "curatedTCGAData", "doParallel", "dplyr", "foreach", "ggplot2", "glmnet", "gridExtra", "httr", "impute", "knitr", "limma", "matrixStats", "readr", "reshape2", "rmarkdown", "tibble"] 89 }, 90 "AMOUNTAIN": { 91 "name": "AMOUNTAIN", 92 "version": "1.36.0", 93 "sha256": "14xmkjysv3ydhqvzc43ld5kl8rl2j08dyykmh4jvi78lm4lwgifs", 94 "depends": [] 95 }, 96 "ANCOMBC": { 97 "name": "ANCOMBC", 98 "version": "2.12.0", 99 "sha256": "1pba6ls61184dx8dyf2lfxcabpnj3av5s60w86104addygnj9y78", 100 "depends": ["CVXR", "DescTools", "Hmisc", "MASS", "Matrix", "Rdpack", "doParallel", "doRNG", "energy", "foreach", "gtools", "lme4", "lmerTest", "multcomp", "nloptr"] 101 }, 102 "ANF": { 103 "name": "ANF", 104 "version": "1.32.0", 105 "sha256": "1l69zjldgvih834k09hfx1lrhj634harva38h983y4cwl58hv4xj", 106 "depends": ["Biobase", "MASS", "RColorBrewer", "igraph", "survival"] 107 }, 108 "APL": { 109 "name": "APL", 110 "version": "1.14.0", 111 "sha256": "0xdj7hwaw3mxqwyv8hd8j37ri4f49ldmv3n4d23n0wm62rrf8igs", 112 "depends": ["Matrix", "RSpectra", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggrepel", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "plotly", "rlang", "topGO", "viridisLite"] 113 }, 114 "ARRmNormalization": { 115 "name": "ARRmNormalization", 116 "version": "1.50.0", 117 "sha256": "0gv4gzva7m77d97aczr44g9xirscwqnib7v9wsld9dd0dsall8mj", 118 "depends": ["ARRmData"] 119 }, 120 "ASAFE": { 121 "name": "ASAFE", 122 "version": "1.36.0", 123 "sha256": "01rdnc6v41ql4bfx4xv23sz67lqm6pgphfd1dskl0rvqnlf8z89p", 124 "depends": [] 125 }, 126 "ASEB": { 127 "name": "ASEB", 128 "version": "1.54.0", 129 "sha256": "03w1pxqyfj92x0bfnxpi9jvshz6vhkp9fgjb0gl8ry1cs7n0n11d", 130 "depends": [] 131 }, 132 "ASGSCA": { 133 "name": "ASGSCA", 134 "version": "1.44.0", 135 "sha256": "1c1172y40jd1apx3vv2mjnhiw87rgv1fhlmnqz7wqkvjil71ial2", 136 "depends": ["MASS", "Matrix"] 137 }, 138 "ASICS": { 139 "name": "ASICS", 140 "version": "2.26.0", 141 "sha256": "01xhk2i13hcbmjy92bxpprn19q64xsqk31f9f7q91rdk4iii0ckd", 142 "depends": ["BiocParallel", "Matrix", "PepsNMR", "SummarizedExperiment", "ggplot2", "glmnet", "gridExtra", "mvtnorm", "plyr", "quadprog", "ropls", "zoo"] 143 }, 144 "ASSET": { 145 "name": "ASSET", 146 "version": "2.28.0", 147 "sha256": "0mg1mmj2wlrwl668vkkxycr5ymzhcai78vvq49hnrrkhnb79wx7h", 148 "depends": ["MASS", "msm", "rmeta"] 149 }, 150 "ASSIGN": { 151 "name": "ASSIGN", 152 "version": "1.46.0", 153 "sha256": "1k38y9nwayrbd0icfqqw2qcpk76g7ycybfnjqfyic6vcgn7yhfr9", 154 "depends": ["Rlab", "ggplot2", "gplots", "msm", "sva", "yaml"] 155 }, 156 "ASURAT": { 157 "name": "ASURAT", 158 "version": "1.14.0", 159 "sha256": "18bb6hx01v1jz4jy0lzr0g0xa269j9jvz8li3wfbfdrnnp0l3cj6", 160 "depends": ["ComplexHeatmap", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "cluster", "plot3D"] 161 }, 162 "ASpli": { 163 "name": "ASpli", 164 "version": "2.20.0", 165 "sha256": "16m8v29f22bwlbz1v5fxhg8rmp2wxaxr9ywl35hpi9jzgbmgpcz5", 166 "depends": ["AnnotationDbi", "BiocGenerics", "BiocStyle", "DT", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "MASS", "Rsamtools", "S4Vectors", "UpSetR", "data_table", "edgeR", "htmltools", "igraph", "limma", "pbmcapply", "tidyr", "txdbmaker"] 167 }, 168 "ATACseqQC": { 169 "name": "ATACseqQC", 170 "version": "1.34.0", 171 "sha256": "0yb69k9cl1ibf8v0jmmzij7l6iz85gf4dyz7yli1b72yf765q5y0", 172 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "ChIPpeakAnno", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "GenomicScores", "IRanges", "KernSmooth", "Rsamtools", "S4Vectors", "edgeR", "limma", "motifStack", "preseqR", "randomForest", "rtracklayer"] 173 }, 174 "ATACseqTFEA": { 175 "name": "ATACseqTFEA", 176 "version": "1.12.0", 177 "sha256": "1zlwbx1pvq5wfxvm94mgdwvy8k53n74bjgzbpp6p34zy5v1cga5r", 178 "depends": ["BiocGenerics", "GenomicAlignments", "GenomicRanges", "IRanges", "Matrix", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TFBSTools", "dplyr", "ggplot2", "ggrepel", "limma", "motifmatchr", "pracma", "rtracklayer"] 179 }, 180 "AUCell": { 181 "name": "AUCell", 182 "version": "1.32.0", 183 "sha256": "1qpdvia2qlq0w477xdia05alfmmnwf0ix2f7ib9hn593fzrp1py7", 184 "depends": ["BiocGenerics", "DelayedArray", "DelayedMatrixStats", "GSEABase", "Matrix", "R_utils", "SummarizedExperiment", "data_table", "mixtools"] 185 }, 186 "AWAggregator": { 187 "name": "AWAggregator", 188 "version": "1.0.0", 189 "sha256": "06czqk7n4gcxw27qzsia6vnibm2mbd1g1315kxgxnivxh9sjsn0k", 190 "depends": ["Peptides", "dplyr", "progress", "purrr", "ranger", "rlang", "stringr", "tidyr", "toOrdinal"] 191 }, 192 "AWFisher": { 193 "name": "AWFisher", 194 "version": "1.24.0", 195 "sha256": "1gllng75bk3iiwrv3r4fphhnx90xk88jll00zja2akxxn0nka2g5", 196 "depends": ["edgeR", "limma"] 197 }, 198 "AffiXcan": { 199 "name": "AffiXcan", 200 "version": "1.28.0", 201 "sha256": "1smbwpp1iqlch3135rkah68bnfh54849yhy8mwj0845i9y9rdqk9", 202 "depends": ["BiocParallel", "MultiAssayExperiment", "SummarizedExperiment", "crayon"] 203 }, 204 "AffyRNADegradation": { 205 "name": "AffyRNADegradation", 206 "version": "1.56.0", 207 "sha256": "11isb0is2l9yccgr61asbf5kyckv2hp64axwv7ncvzrq6gn6zqy6", 208 "depends": ["affy"] 209 }, 210 "AgiMicroRna": { 211 "name": "AgiMicroRna", 212 "version": "2.60.0", 213 "sha256": "0an7hfccdcxcsshafihhib77x96f5a0lny28zdnsi31dx41mmpvh", 214 "depends": ["Biobase", "affy", "affycoretools", "limma", "preprocessCore"] 215 }, 216 "AllelicImbalance": { 217 "name": "AllelicImbalance", 218 "version": "1.48.0", 219 "sha256": "0g4gv0h69cld903nb0sr58vc7vsbkr62p19m7fjfhv0crmkr960s", 220 "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "gridExtra", "lattice", "latticeExtra", "nlme", "seqinr"] 221 }, 222 "AlphaBeta": { 223 "name": "AlphaBeta", 224 "version": "1.24.0", 225 "sha256": "0s550vmcsnm2ih1vajyah8kqvk7y4bgyrwm1fddzvqsizn3w61x1", 226 "depends": ["BiocParallel", "data_table", "dplyr", "expm", "ggplot2", "gtools", "igraph", "optimx", "plotly", "stringr"] 227 }, 228 "AlphaMissenseR": { 229 "name": "AlphaMissenseR", 230 "version": "1.6.0", 231 "sha256": "1d36bav4fn5dmay9c9czb19b15yx0lvh13l2h6irw15i0q38480a", 232 "depends": ["BiocBaseUtils", "BiocFileCache", "DBI", "curl", "dplyr", "duckdb", "ggplot2", "memoise", "rjsoncons", "rlang", "spdl", "whisker"] 233 }, 234 "AlpsNMR": { 235 "name": "AlpsNMR", 236 "version": "4.12.0", 237 "sha256": "0bfx721f9bx22xls65d1ygdkwbh1xadnff6nw29gyk7yic62nwik", 238 "depends": ["BiocParallel", "baseline", "cli", "dplyr", "fs", "generics", "ggplot2", "glue", "htmltools", "magrittr", "matrixStats", "mixOmics", "pcaPP", "purrr", "readxl", "reshape2", "rlang", "rmarkdown", "scales", "signal", "speaq", "stringr", "tibble", "tidyr", "tidyselect", "vctrs"] 239 }, 240 "AnVIL": { 241 "name": "AnVIL", 242 "version": "1.22.0", 243 "sha256": "08r41q8zb72kbfslw851152h4k2q7jzkk0d85d6rmvdd3r1qd9bw", 244 "depends": ["AnVILBase", "BiocBaseUtils", "DT", "GCPtools", "dplyr", "futile_logger", "htmltools", "httr", "jsonlite", "miniUI", "rapiclient", "shiny", "tibble", "yaml"] 245 }, 246 "AnVILAz": { 247 "name": "AnVILAz", 248 "version": "1.4.0", 249 "sha256": "0hzmqbqrak5b0y3872mcddd3568dmxi9456qv8svsjqp2bg4941v", 250 "depends": ["AnVILBase", "BiocBaseUtils", "curl", "httr2", "jsonlite", "rjsoncons", "tibble"] 251 }, 252 "AnVILBase": { 253 "name": "AnVILBase", 254 "version": "1.4.0", 255 "sha256": "12bv85l363a6zy3jmsp2rqcyhha5slqmalyyc9dzxyk6s47qg9rh", 256 "depends": ["dplyr", "httr", "httr2", "jsonlite", "tibble"] 257 }, 258 "AnVILBilling": { 259 "name": "AnVILBilling", 260 "version": "1.20.0", 261 "sha256": "0w8j6wgpi614mqs850x20c1pwi4za11gyyjnlsms22b5dv0vnsqp", 262 "depends": ["DBI", "DT", "bigrquery", "dplyr", "ggplot2", "lubridate", "magrittr", "plotly", "shiny", "shinytoastr"] 263 }, 264 "AnVILGCP": { 265 "name": "AnVILGCP", 266 "version": "1.4.0", 267 "sha256": "151gklrnpwdj3mdlxn71q4nh01xxl76xqljmk551dqyzpi9qic8i", 268 "depends": ["AnVILBase", "BiocBaseUtils", "GCPtools", "dplyr", "httr", "jsonlite", "rlang", "tibble", "tidyr"] 269 }, 270 "AnVILPublish": { 271 "name": "AnVILPublish", 272 "version": "1.20.0", 273 "sha256": "1x60vfhs9w60kc3ibgc7f6hzzfzzgq40g186zvwwa7fbkm44yhiw", 274 "depends": ["AnVIL", "AnVILGCP", "BiocBaseUtils", "BiocManager", "httr", "jsonlite", "readr", "rmarkdown", "whisker", "yaml"] 275 }, 276 "AnVILWorkflow": { 277 "name": "AnVILWorkflow", 278 "version": "1.10.0", 279 "sha256": "1i7pia3hgr4is23vyligxbkr3a8qr935w4nx2z5ig645k4wk9q0g", 280 "depends": ["AnVIL", "AnVILBase", "AnVILGCP", "dplyr", "httr", "jsonlite", "plyr", "rlang", "stringr", "tibble", "tidyr"] 281 }, 282 "Anaquin": { 283 "name": "Anaquin", 284 "version": "2.34.0", 285 "sha256": "159hipdjikaflrpz79xsvx8ks97c7r8ibnzhj90vya3jf2vfvaq3", 286 "depends": ["DESeq2", "ROCR", "ggplot2", "knitr", "locfit", "plyr", "qvalue"] 287 }, 288 "AnnotationDbi": { 289 "name": "AnnotationDbi", 290 "version": "1.72.0", 291 "sha256": "0vzrkx8x060281zmk13k8ajrfl8g6sx361563yw4aymvjdrdax37", 292 "depends": ["Biobase", "BiocGenerics", "DBI", "IRanges", "KEGGREST", "RSQLite", "S4Vectors"] 293 }, 294 "AnnotationFilter": { 295 "name": "AnnotationFilter", 296 "version": "1.34.0", 297 "sha256": "1p8m3kx6il3g1pfc3d7kxqvpdr1dpalscp7pav03a1v3x7199gn5", 298 "depends": ["GenomicRanges", "lazyeval"] 299 }, 300 "AnnotationForge": { 301 "name": "AnnotationForge", 302 "version": "1.52.0", 303 "sha256": "0idd80w57yd4gxv5k15mzwmny18bsv2aphx7zkk250nbhj9qb7l7", 304 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "RCurl", "RSQLite", "S4Vectors", "XML"] 305 }, 306 "AnnotationHub": { 307 "name": "AnnotationHub", 308 "version": "4.0.0", 309 "sha256": "1im0k4ajrpvmvlyi0v76x93mzwq77nq9mx1rwq3x7xfr5hz6r21f", 310 "depends": ["AnnotationDbi", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "RSQLite", "S4Vectors", "curl", "dplyr", "httr2", "rappdirs", "yaml"] 311 }, 312 "AnnotationHubData": { 313 "name": "AnnotationHubData", 314 "version": "1.40.0", 315 "sha256": "1ix1mnl0ai16160rfghcn6apckdicm2hnafch8b0yf50iz5sg5fk", 316 "depends": ["AnnotationDbi", "AnnotationForge", "AnnotationHub", "Biobase", "BiocCheck", "BiocGenerics", "BiocManager", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "OrganismDbi", "RCurl", "RSQLite", "Rsamtools", "S4Vectors", "Seqinfo", "XML", "biocViews", "futile_logger", "graph", "jsonlite", "rtracklayer"] 317 }, 318 "ArrayExpress": { 319 "name": "ArrayExpress", 320 "version": "1.70.0", 321 "sha256": "1f7ai8ljy6ssbk21fl2f565v988ry12k5x7ima73z0a378zq8dyb", 322 "depends": ["Biobase", "httr", "jsonlite", "limma", "oligo", "rlang"] 323 }, 324 "AssessORF": { 325 "name": "AssessORF", 326 "version": "1.28.0", 327 "sha256": "16020ypgrahjcmfw46lniqabb6c0bghsw6vznxxm98bakcqv0qlz", 328 "depends": ["Biostrings", "DECIPHER", "GenomicRanges", "IRanges"] 329 }, 330 "BADER": { 331 "name": "BADER", 332 "version": "1.48.0", 333 "sha256": "1kxdwxr5hfdgky2083jp1cy79qilv1lb3l1ccpx0y0khf8104nld", 334 "depends": [] 335 }, 336 "BAGS": { 337 "name": "BAGS", 338 "version": "2.50.0", 339 "sha256": "0813s292xszlw4r8xy0hnm0jkawz6l7cafv2xsa7k005lzm6dhbx", 340 "depends": ["Biobase", "breastCancerVDX"] 341 }, 342 "BANDITS": { 343 "name": "BANDITS", 344 "version": "1.26.0", 345 "sha256": "0ygh1sgnxsqvz9k79sp29nc1rvm4cfp7g1fxy0hiis9p6lznz88m", 346 "depends": ["BiocParallel", "DRIMSeq", "MASS", "R_utils", "Rcpp", "RcppArmadillo", "data_table", "doParallel", "doRNG", "foreach", "ggplot2"] 347 }, 348 "BASiCS": { 349 "name": "BASiCS", 350 "version": "2.22.0", 351 "sha256": "04z4dphnxvphhngxqd7zcv5072s424m08vdsk7aqiyv7zd63jacz", 352 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "assertthat", "coda", "cowplot", "ggExtra", "ggplot2", "hexbin", "matrixStats", "posterior", "reshape2", "scran", "scuttle", "viridis"] 353 }, 354 "BASiCStan": { 355 "name": "BASiCStan", 356 "version": "1.12.0", 357 "sha256": "05iinqlg0jfsc1fs2sdbxkyizh04myspp9fax4jimpwys0svp8im", 358 "depends": ["BASiCS", "BH", "Rcpp", "RcppEigen", "RcppParallel", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "glmGamPoi", "rstan", "rstantools", "scran", "scuttle"] 359 }, 360 "BBCAnalyzer": { 361 "name": "BBCAnalyzer", 362 "version": "1.40.0", 363 "sha256": "0dsfj212y0gh2njch10hrzhdl63h12qkhky2n3slq3kp0qzvi5gk", 364 "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation"] 365 }, 366 "BCRANK": { 367 "name": "BCRANK", 368 "version": "1.72.0", 369 "sha256": "0snryc43qkhcgaaymdxrfviyg700zvq32s7y3pl649l4qnvr0y4p", 370 "depends": ["Biostrings"] 371 }, 372 "BEAT": { 373 "name": "BEAT", 374 "version": "1.48.0", 375 "sha256": "0d7jmn0w9yj09b14ylfsfqqivqkx55agmc1wk20cnrcisypfmi24", 376 "depends": ["BSgenome", "Biostrings", "GenomicRanges", "ShortRead"] 377 }, 378 "BERT": { 379 "name": "BERT", 380 "version": "1.6.0", 381 "sha256": "0dif7q6cg6pz56yvwwg1zghv7n9b8gk0wc4j8lxpx1pn16pslqpl", 382 "depends": ["BiocParallel", "SummarizedExperiment", "cluster", "comprehenr", "foreach", "invgamma", "iterators", "janitor", "limma", "logging", "sva"] 383 }, 384 "BEclear": { 385 "name": "BEclear", 386 "version": "2.26.0", 387 "sha256": "08q3hzyrbx3b34dgjh21q0wvz7489y7y0d3z3syg76hpgsmbqa61", 388 "depends": ["BiocParallel", "Matrix", "Rcpp", "Rdpack", "abind", "data_table", "dixonTest", "futile_logger", "ids"] 389 }, 390 "BG2": { 391 "name": "BG2", 392 "version": "1.10.0", 393 "sha256": "1h4i0bavsqlhgqjz1j6ihaz3247gg7d2n9gv6ssmqsrmgfr1kfcd", 394 "depends": ["GA", "MASS", "Matrix", "caret", "memoise"] 395 }, 396 "BLMA": { 397 "name": "BLMA", 398 "version": "1.34.0", 399 "sha256": "1r5bxljaqvx145k78n3q1mrjksfjbyng63wsn9y8xwcjiwfzj84j", 400 "depends": ["Biobase", "GSA", "PADOG", "ROntoTools", "graph", "limma", "metafor"] 401 }, 402 "BOBaFIT": { 403 "name": "BOBaFIT", 404 "version": "1.14.0", 405 "sha256": "0whrk2s02kisrq2f884vw72g5m7z27xb12498l7rr30hynxy0vsw", 406 "depends": ["GenomicRanges", "NbClust", "dplyr", "ggbio", "ggforce", "ggplot2", "magrittr", "plyranges", "stringr", "tidyr"] 407 }, 408 "BRAIN": { 409 "name": "BRAIN", 410 "version": "1.56.0", 411 "sha256": "1dimjgbl3rzqgbqq1c2s7ksv3f6hi8ghpgrhv6brnp7b04mjzbxc", 412 "depends": ["Biostrings", "PolynomF", "lattice"] 413 }, 414 "BREW3R_r": { 415 "name": "BREW3R.r", 416 "version": "1.6.0", 417 "sha256": "143c7kpn6k2ayj8h0n1jwd7kw4ss44x73sk7ja5k03j2n257yya4", 418 "depends": ["GenomicRanges", "S4Vectors", "rlang"] 419 }, 420 "BSgenome": { 421 "name": "BSgenome", 422 "version": "1.78.0", 423 "sha256": "05j4nd6n7g0a5jprn2sq2ki0fwzca4hj850gazr3xh6a461ggjgi", 424 "depends": ["BiocGenerics", "BiocIO", "Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "XVector", "matrixStats", "rtracklayer"] 425 }, 426 "BSgenomeForge": { 427 "name": "BSgenomeForge", 428 "version": "1.10.0", 429 "sha256": "0g3wh1i29j5kkf9v1apgix8268ylmn8yhksibwkkpnhvwz9c2dj7", 430 "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocIO", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "rtracklayer"] 431 }, 432 "BUMHMM": { 433 "name": "BUMHMM", 434 "version": "1.34.0", 435 "sha256": "018p00njamj3dicbky2mpq944wlnc1p6mjmprndl3118zcxpv2i1", 436 "depends": ["Biostrings", "IRanges", "SummarizedExperiment", "devtools", "gtools", "stringi"] 437 }, 438 "BUS": { 439 "name": "BUS", 440 "version": "1.66.0", 441 "sha256": "0nmqym06q9v6cvfw5yi0fv623q1j8xsfkwsk0pbx1dazcav9b2mp", 442 "depends": ["infotheo", "minet"] 443 }, 444 "BUScorrect": { 445 "name": "BUScorrect", 446 "version": "1.28.0", 447 "sha256": "1j46hlzay56mpj1pr4vcgq89j7q0pyx20kj6ymhpxqmhf2ax9077", 448 "depends": ["SummarizedExperiment", "gplots"] 449 }, 450 "BUSpaRse": { 451 "name": "BUSpaRse", 452 "version": "1.24.0", 453 "sha256": "0907sj9icf5ywn6rbcrk37wpp8njiyyxq5fkq76wzzj5v6m96n75", 454 "depends": ["AnnotationDbi", "AnnotationFilter", "AnnotationHub", "BH", "BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "RcppArmadillo", "RcppProgress", "S4Vectors", "biomaRt", "dplyr", "ensembldb", "ggplot2", "lifecycle", "magrittr", "plyranges", "stringr", "tibble", "tidyr", "zeallot"] 455 }, 456 "BUSseq": { 457 "name": "BUSseq", 458 "version": "1.16.0", 459 "sha256": "0iw84pf59zf39ldbibl4qxyjvn9id86xrnvalryvs1mpjdazyjb2", 460 "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "gplots"] 461 }, 462 "BaalChIP": { 463 "name": "BaalChIP", 464 "version": "1.36.0", 465 "sha256": "0zi2b93jrcv5y7462f2bcdp768pik78n5nxwwrd3y5w46j8k7l7k", 466 "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "coda", "doBy", "doParallel", "foreach", "ggplot2", "reshape2", "scales"] 467 }, 468 "BadRegionFinder": { 469 "name": "BadRegionFinder", 470 "version": "1.38.0", 471 "sha256": "0413bc39r666dwgyhskdllvyqfvxvh2hna535mnjm1326wprhvcz", 472 "depends": ["GenomicRanges", "Rsamtools", "S4Vectors", "VariantAnnotation", "biomaRt"] 473 }, 474 "Banksy": { 475 "name": "Banksy", 476 "version": "1.6.0", 477 "sha256": "02bhdxckryvnilq7hsbngy6g251cnjg4j9d7wg4m3gkrcsrbjwim", 478 "depends": ["BiocParallel", "GenomeInfoDb", "Matrix", "MatrixGenerics", "RcppHungarian", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "aricode", "data_table", "dbscan", "igraph", "irlba", "leidenAlg", "mclust", "uwot"] 479 }, 480 "BaseSpaceR": { 481 "name": "BaseSpaceR", 482 "version": "1.54.0", 483 "sha256": "0dyv8abr34jhig7xb7z7gghb0nnqaflwqshqbls08layz5wh4p21", 484 "depends": ["RCurl", "RJSONIO"] 485 }, 486 "Basic4Cseq": { 487 "name": "Basic4Cseq", 488 "version": "1.46.0", 489 "sha256": "1jjmsn2dryvkyisbw4jwq8df162wkmcr7kiqn8jwz9g4gzi8lb6b", 490 "depends": ["BSgenome_Ecoli_NCBI_20080805", "Biostrings", "GenomicAlignments", "GenomicRanges", "RCircos", "caTools"] 491 }, 492 "BasicSTARRseq": { 493 "name": "BasicSTARRseq", 494 "version": "1.38.0", 495 "sha256": "06yxawx34bfr1112kkrd1g7n27qfxrnxq699ap18469vxypz2dw8", 496 "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo"] 497 }, 498 "BatchQC": { 499 "name": "BatchQC", 500 "version": "2.6.0", 501 "sha256": "12igzinwk2lkxkrsbxpm59jqizw0walvr7xrhhl18hjjfalff7ji", 502 "depends": ["DESeq2", "EBSeq", "FNN", "MASS", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "edgeR", "ggdendro", "ggnewscale", "ggplot2", "limma", "matrixStats", "pheatmap", "reader", "reshape2", "scran", "shiny", "shinyjs", "shinythemes", "sva", "tibble", "tidyr", "tidyverse", "umap"] 503 }, 504 "BatchSVG": { 505 "name": "BatchSVG", 506 "version": "1.2.0", 507 "sha256": "005dk3aijcm881fdy35mqhrchh34i057c3x9n168g4lp3h4k036r", 508 "depends": ["RColorBrewer", "SummarizedExperiment", "cowplot", "dplyr", "ggplot2", "ggrepel", "rlang", "scales", "scry"] 509 }, 510 "BayesKnockdown": { 511 "name": "BayesKnockdown", 512 "version": "1.36.0", 513 "sha256": "1a69cywgxsfylm4nvidllqnh9pgkps7lw15c62zpbh9jk041fxad", 514 "depends": ["Biobase"] 515 }, 516 "BayesSpace": { 517 "name": "BayesSpace", 518 "version": "1.20.0", 519 "sha256": "1mqa0f08ynpplvg7ni8alk0a9w4yy876jslzx3p1kmyb8ncb4zaj", 520 "depends": ["BiocFileCache", "BiocParallel", "BiocSingular", "DirichletReg", "Matrix", "RCurl", "Rcpp", "RcppArmadillo", "RcppDist", "RcppProgress", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "arrow", "assertthat", "coda", "dplyr", "ggplot2", "magrittr", "mclust", "microbenchmark", "purrr", "rhdf5", "rjson", "rlang", "scales", "scater", "scran", "tibble", "tidyr", "xgboost"] 521 }, 522 "BeadDataPackR": { 523 "name": "BeadDataPackR", 524 "version": "1.62.0", 525 "sha256": "0dl1clwaccv0s7g5ka27wrb74yw8pm1sy12ax4fkpmdbyka7ca19", 526 "depends": [] 527 }, 528 "BgeeCall": { 529 "name": "BgeeCall", 530 "version": "1.26.0", 531 "sha256": "1ql6id4l1qchavywbarj0c5vc8j7ars34br9wb4s66is68bb688p", 532 "depends": ["AnnotationDbi", "Biostrings", "GenomicFeatures", "IRanges", "RCurl", "RSQLite", "curl", "data_table", "dplyr", "ggplot2", "jsonlite", "readr", "rhdf5", "rslurm", "rtracklayer", "scales", "sjmisc", "spatstat_univar", "stringr", "txdbmaker", "tximport"] 533 }, 534 "BgeeDB": { 535 "name": "BgeeDB", 536 "version": "2.36.0", 537 "sha256": "0a0ldkaibca8iipnyhy8h55za3acii4vchssk497bl0788gybbsc", 538 "depends": ["Biobase", "HDF5Array", "RCurl", "RSQLite", "R_utils", "anndata", "bread", "curl", "data_table", "digest", "dplyr", "graph", "tidyr", "topGO", "zellkonverter"] 539 }, 540 "BiFET": { 541 "name": "BiFET", 542 "version": "1.30.0", 543 "sha256": "08w0jfilp954k82px74ppmr7h2k1mzac1788bbp5qdq50vym4iks", 544 "depends": ["GenomicRanges", "poibin"] 545 }, 546 "BiRewire": { 547 "name": "BiRewire", 548 "version": "3.41.0", 549 "sha256": "18ckdn0ls29z7i51k6ilnd4d65ci33zcy9lidmr34djyjh732b4v", 550 "depends": ["Matrix", "Rtsne", "igraph", "slam"] 551 }, 552 "BiSeq": { 553 "name": "BiSeq", 554 "version": "1.50.0", 555 "sha256": "0j2v6ppb28rf2l3i8jm2afqxban8fpwh83rr5mrvxc5l90i7j1bd", 556 "depends": ["Biobase", "BiocGenerics", "Formula", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "SummarizedExperiment", "betareg", "globaltest", "lokern", "rtracklayer"] 557 }, 558 "BicARE": { 559 "name": "BicARE", 560 "version": "1.68.0", 561 "sha256": "1jw4ldm5mhzzcxymdhyqydryxxj5chcs85x3wy5f658vnwb8v1zc", 562 "depends": ["Biobase", "GO_db", "GSEABase", "multtest"] 563 }, 564 "BindingSiteFinder": { 565 "name": "BindingSiteFinder", 566 "version": "2.8.0", 567 "sha256": "17fl66fqbyibhgyjisfvjjmprpk1l6vw5mbb67j29skgnyv0882n", 568 "depends": ["ComplexHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "dplyr", "forcats", "ggdist", "ggforce", "ggplot2", "kableExtra", "lifecycle", "matrixStats", "plyr", "rlang", "rtracklayer", "tibble", "tidyr"] 569 }, 570 "BioCartaImage": { 571 "name": "BioCartaImage", 572 "version": "1.8.0", 573 "sha256": "1p65sdfhsq2iwg87mmxb95r7z92jyrw6b7qxxy3rjb9iwzxqyzc1", 574 "depends": ["magick"] 575 }, 576 "BioCor": { 577 "name": "BioCor", 578 "version": "1.34.0", 579 "sha256": "04bfi8mmff5ykxim1rzpfgglbcdy6aj1ha9l86cb6pp40ssp8rn5", 580 "depends": ["BiocParallel", "GSEABase", "Matrix"] 581 }, 582 "BioGA": { 583 "name": "BioGA", 584 "version": "1.4.0", 585 "sha256": "0pyylg02l6fsdnmyhmqajy4jlqa2m1xwdkdrdyzqk3cyqp2mrf20", 586 "depends": ["BiocStyle", "Rcpp", "SummarizedExperiment", "animation", "biocViews", "ggplot2", "rlang", "sessioninfo"] 587 }, 588 "BioMVCClass": { 589 "name": "BioMVCClass", 590 "version": "1.78.0", 591 "sha256": "0iiz1akgb43kwsk1s318m7scwirksvjbd9kkjv246rpnagwi3im4", 592 "depends": ["Biobase", "MVCClass", "Rgraphviz", "graph"] 593 }, 594 "BioNAR": { 595 "name": "BioNAR", 596 "version": "1.11.0", 597 "sha256": "0sfrkliw433lr5bb7hi39nbajvn003dcfr6wj1rg8vfbny9hb1bn", 598 "depends": ["AnnotationDbi", "GO_db", "Matrix", "RSpectra", "Rdpack", "WGCNA", "cowplot", "data_table", "dplyr", "fgsea", "ggplot2", "ggrepel", "igraph", "latex2exp", "minpack_lm", "org_Hs_eg_db", "poweRlaw", "rSpectral", "scales", "stringr", "viridis"] 599 }, 600 "BioNERO": { 601 "name": "BioNERO", 602 "version": "1.18.0", 603 "sha256": "1sx68jlh98as80hkwdl6bd0xzdf3qc0cydg3xl8x4zv4wbs03mzy", 604 "depends": ["BiocParallel", "ComplexHeatmap", "GENIE3", "NetRep", "RColorBrewer", "SummarizedExperiment", "WGCNA", "dynamicTreeCut", "ggdendro", "ggnetwork", "ggplot2", "ggrepel", "igraph", "intergraph", "matrixStats", "minet", "patchwork", "reshape2", "rlang", "sva"] 605 }, 606 "BioNet": { 607 "name": "BioNet", 608 "version": "1.70.0", 609 "sha256": "1kdx2ib8bki02qszvysqvpq0pj70z1dkinqpzhqvys73kdwpqz3g", 610 "depends": ["AnnotationDbi", "Biobase", "RBGL", "graph", "igraph"] 611 }, 612 "BioQC": { 613 "name": "BioQC", 614 "version": "1.38.0", 615 "sha256": "16v51mhmf1pns9ym4crqd0k5swnkmj5gir3rb17j6mcv9s904x7d", 616 "depends": ["Biobase", "Rcpp", "edgeR"] 617 }, 618 "BioTIP": { 619 "name": "BioTIP", 620 "version": "1.24.0", 621 "sha256": "0chi6b3ygglll9pfl0i2jhq5sadzhzll2fvxc7gifvfjk4pzqk3a", 622 "depends": ["GenomicRanges", "MASS", "cluster", "doParallel", "foreach", "igraph", "psych", "scran", "stringr"] 623 }, 624 "Biobase": { 625 "name": "Biobase", 626 "version": "2.70.0", 627 "sha256": "1g1wh5brsspnjxxnxa0jjp3nl15m7254rk3bn56w71hfchsp82jk", 628 "depends": ["BiocGenerics"] 629 }, 630 "Bioc_gff": { 631 "name": "Bioc.gff", 632 "version": "1.0.0", 633 "sha256": "0729zbfvhlbzir5icw1ixy46wabl19bi1l5x78hdgffpg8c66m5x", 634 "depends": ["BiocBaseUtils", "BiocGenerics", "BiocIO", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "XVector", "curl"] 635 }, 636 "BiocBaseUtils": { 637 "name": "BiocBaseUtils", 638 "version": "1.12.0", 639 "sha256": "06ha45xxmh0jmk0jvjarf8151vlr6aw8j5a58krckk2n5y9chk48", 640 "depends": [] 641 }, 642 "BiocBook": { 643 "name": "BiocBook", 644 "version": "1.8.0", 645 "sha256": "0hsbfx3v9bx3lma7v7bnkc4bgixdhgbz3ynxq250zbarrd9vry0b", 646 "depends": ["BiocGenerics", "cli", "dplyr", "gert", "gh", "gitcreds", "glue", "httr", "pak", "purrr", "quarto", "renv", "rlang", "rprojroot", "stringr", "tibble", "usethis", "yaml"] 647 }, 648 "BiocCheck": { 649 "name": "BiocCheck", 650 "version": "1.46.0", 651 "sha256": "0fb114cdk8xl9r4kgvril4b8zw082f32mdrxwk564byz5r5r41cl", 652 "depends": ["BiocBaseUtils", "BiocFileCache", "BiocManager", "biocViews", "callr", "cli", "codetools", "graph", "httr2", "knitr", "rvest", "stringdist"] 653 }, 654 "BiocFHIR": { 655 "name": "BiocFHIR", 656 "version": "1.12.0", 657 "sha256": "0b8q7v68h22nzby9b54kz058yvk59wkxww04j886bdjsi4lp46cd", 658 "depends": ["BiocBaseUtils", "DT", "dplyr", "graph", "jsonlite", "shiny", "tidyr", "visNetwork"] 659 }, 660 "BiocFileCache": { 661 "name": "BiocFileCache", 662 "version": "3.0.0", 663 "sha256": "0gcrvmbqbic7jwk3cnd004d57mazd4ynp2p72l24b7dnrl10ggqm", 664 "depends": ["DBI", "RSQLite", "curl", "dbplyr", "dplyr", "filelock", "httr2"] 665 }, 666 "BiocGenerics": { 667 "name": "BiocGenerics", 668 "version": "0.56.0", 669 "sha256": "1q38kdnnlndjbp5zzsfw0a0hkih08ivlqbsxz66s8rx77kv5yy8p", 670 "depends": ["generics"] 671 }, 672 "BiocHail": { 673 "name": "BiocHail", 674 "version": "1.10.0", 675 "sha256": "1qh7vdkpdll2l6ghhcdp8m17bcn9y0yd5r2jcm33qgf3xwg0l1pc", 676 "depends": ["BiocFileCache", "BiocGenerics", "basilisk", "dplyr", "reticulate"] 677 }, 678 "BiocHubsShiny": { 679 "name": "BiocHubsShiny", 680 "version": "1.10.0", 681 "sha256": "0ffskx4zg1hcb7avaipvgaj3m3ybwmjsp34i9hng6z9x9ivxyzx6", 682 "depends": ["AnnotationHub", "DT", "ExperimentHub", "S4Vectors", "htmlwidgets", "rclipboard", "shiny", "shinyAce", "shinybiocloader", "shinyjs", "shinythemes"] 683 }, 684 "BiocIO": { 685 "name": "BiocIO", 686 "version": "1.20.0", 687 "sha256": "12yd8dqs8flcq8k9f5ndk4kyjccm4bw1ml2mn7na4zyi14xq8xw1", 688 "depends": ["BiocGenerics", "S4Vectors"] 689 }, 690 "BiocNeighbors": { 691 "name": "BiocNeighbors", 692 "version": "2.4.0", 693 "sha256": "1yx09x4rg254gl34kqzx1hqky7y3waxbmcqhnvss6n3wrbswfrvk", 694 "depends": ["Rcpp", "assorthead"] 695 }, 696 "BiocParallel": { 697 "name": "BiocParallel", 698 "version": "1.44.0", 699 "sha256": "1hi3k85ywc8r0sw6fys4987j8mr5vhkha4bcb3hc5fdfnpk6j81v", 700 "depends": ["BH", "codetools", "cpp11", "futile_logger", "snow"] 701 }, 702 "BiocPkgTools": { 703 "name": "BiocPkgTools", 704 "version": "1.27.12", 705 "sha256": "03z6b711071k15j8vlm4zgb36vli3y3zh1lnglz1xyimmvhvn9cp", 706 "depends": ["BiocFileCache", "BiocManager", "DT", "RBGL", "biocViews", "curl", "dplyr", "gh", "glue", "graph", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "jsonlite", "lubridate", "purrr", "readr", "rlang", "rvest", "stringr", "tibble", "tidyr", "xml2", "yaml"] 707 }, 708 "BiocSet": { 709 "name": "BiocSet", 710 "version": "1.24.0", 711 "sha256": "06mjk88gm562rmnzb3bj56s5cc4griwlisvv5x4f3av9xlks7mam", 712 "depends": ["AnnotationDbi", "BiocIO", "KEGGREST", "S4Vectors", "dplyr", "ontologyIndex", "plyr", "rlang", "tibble", "tidyr"] 713 }, 714 "BiocSingular": { 715 "name": "BiocSingular", 716 "version": "1.26.0", 717 "sha256": "0qyb6a9qay1my04ni2xwpkln5rinlyryhl6x66nqcrv56q8kig5y", 718 "depends": ["BiocGenerics", "BiocParallel", "DelayedArray", "Matrix", "Rcpp", "S4Vectors", "ScaledMatrix", "assorthead", "beachmat", "irlba", "rsvd"] 719 }, 720 "BiocSklearn": { 721 "name": "BiocSklearn", 722 "version": "1.32.0", 723 "sha256": "0963xw4vyqlsmmg7i8xk0wb1md3z65znvbyh3i5bzidbnwfi0lmk", 724 "depends": ["SummarizedExperiment", "basilisk", "reticulate"] 725 }, 726 "BiocStyle": { 727 "name": "BiocStyle", 728 "version": "2.38.0", 729 "sha256": "0817kgf3d1lsqsg7a3vg5vrb9ia6g4j3x25cfk3j3sg64w3wz158", 730 "depends": ["BiocManager", "bookdown", "knitr", "rmarkdown", "yaml"] 731 }, 732 "BiocVersion": { 733 "name": "BiocVersion", 734 "version": "3.22.0", 735 "sha256": "1113nqcv5xr2w1rj8vd4sq4a086fwwmgr6b6zv7aisi2hzqbv2j4", 736 "depends": [] 737 }, 738 "BiocWorkflowTools": { 739 "name": "BiocWorkflowTools", 740 "version": "1.36.0", 741 "sha256": "1jnch9vbfg4qw912wki4fs60gwjmwia3zksc75lk65wr6q57ibq4", 742 "depends": ["BiocStyle", "bookdown", "git2r", "httr", "knitr", "rmarkdown", "rstudioapi", "stringr", "usethis"] 743 }, 744 "Biostrings": { 745 "name": "Biostrings", 746 "version": "2.78.0", 747 "sha256": "11fn7wiw3simgkgk2hka7aiac7n5hnzhjpjfl0ybx8820a76daxk", 748 "depends": ["BiocGenerics", "IRanges", "S4Vectors", "Seqinfo", "XVector", "crayon"] 749 }, 750 "BloodGen3Module": { 751 "name": "BloodGen3Module", 752 "version": "1.18.0", 753 "sha256": "0d43amxrmab12xzdrir3xyw03wpkixxc4vz20n50h7ar2wp82cfg", 754 "depends": ["ComplexHeatmap", "ExperimentHub", "SummarizedExperiment", "V8", "circlize", "ggplot2", "gtools", "limma", "matrixStats", "preprocessCore", "randomcoloR", "reshape2", "testthat"] 755 }, 756 "BreastSubtypeR": { 757 "name": "BreastSubtypeR", 758 "version": "1.2.0", 759 "sha256": "03v3ql4lrq7wz4aszyg5ssjqyf6nk33jp1xf5f1nsfm2jn9zqvqn", 760 "depends": ["Biobase", "ComplexHeatmap", "RColorBrewer", "SummarizedExperiment", "circlize", "data_table", "dplyr", "e1071", "edgeR", "ggplot2", "ggrepel", "impute", "magrittr", "rlang", "stringr", "tidyselect", "withr"] 761 }, 762 "BridgeDbR": { 763 "name": "BridgeDbR", 764 "version": "2.20.0", 765 "sha256": "1znqm7djm0qapf6bg9z8y7h0hyp78b9831g8i2g4h87qn937s6mg", 766 "depends": ["curl", "rJava"] 767 }, 768 "BrowserViz": { 769 "name": "BrowserViz", 770 "version": "2.32.0", 771 "sha256": "13qgng7innngs46x2zkng4irsn476crqn2f6a4qd48gc503ynpai", 772 "depends": ["BiocGenerics", "httpuv", "jsonlite"] 773 }, 774 "BufferedMatrix": { 775 "name": "BufferedMatrix", 776 "version": "1.74.0", 777 "sha256": "1fig1pjpvr2zkbp4kypr9bbyp8774sq7lxvr6ianw5ikbp5pf9jv", 778 "depends": [] 779 }, 780 "BufferedMatrixMethods": { 781 "name": "BufferedMatrixMethods", 782 "version": "1.74.0", 783 "sha256": "1x3pizdv9p6axg08h5pk7wqw851rq7djymr9c9r7fpwnkqbfiv7k", 784 "depends": ["BufferedMatrix"] 785 }, 786 "BulkSignalR": { 787 "name": "BulkSignalR", 788 "version": "1.2.0", 789 "sha256": "0lx8lfkly78cvmlgj9pscavi7is283ppb0jplgvzm15d5is91376", 790 "depends": ["BiocFileCache", "ComplexHeatmap", "RANN", "RCurl", "Rtsne", "SpatialExperiment", "SummarizedExperiment", "circlize", "cli", "curl", "doParallel", "foreach", "ggalluvial", "ggplot2", "ggrepel", "glmnet", "gridExtra", "httr2", "igraph", "jsonlite", "matrixStats", "multtest", "orthogene", "rlang", "scales", "stabledist"] 791 }, 792 "BumpyMatrix": { 793 "name": "BumpyMatrix", 794 "version": "1.18.0", 795 "sha256": "0xz9yqycp91k5m9rf58lp2fvbx44k5lf9wpanrid4v50j82hyipx", 796 "depends": ["IRanges", "Matrix", "S4Vectors"] 797 }, 798 "CAEN": { 799 "name": "CAEN", 800 "version": "1.18.0", 801 "sha256": "0knnz2czma0fx3rv6mdrgqs1d3xn883wy9s74g670x4dswfk3vzg", 802 "depends": ["PoiClaClu", "SummarizedExperiment"] 803 }, 804 "CAFE": { 805 "name": "CAFE", 806 "version": "1.46.0", 807 "sha256": "13nygknhnwczy6zq6xb18in2ji0drv2wz1xk0ynvz1c6dgsyhb6p", 808 "depends": ["Biobase", "GenomicRanges", "IRanges", "affy", "annotate", "biovizBase", "ggbio", "ggplot2", "gridExtra"] 809 }, 810 "CAGEfightR": { 811 "name": "CAGEfightR", 812 "version": "1.30.0", 813 "sha256": "0n2bgzxyhj6pp3zcpk770s0pnhjf25ncgrg0bsxmnr7yl6m7gs4r", 814 "depends": ["BiocGenerics", "BiocParallel", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicInteractions", "GenomicRanges", "Gviz", "IRanges", "InteractionSet", "Matrix", "S4Vectors", "Seqinfo", "SummarizedExperiment", "assertthat", "pryr", "rtracklayer"] 815 }, 816 "CAGEr": { 817 "name": "CAGEr", 818 "version": "2.16.0", 819 "sha256": "1s4fii9m1irymq5nnbffkj66aigz0rdbwgsxcddn6a7lqjz3xndn", 820 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "CAGEfightR", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "KernSmooth", "Matrix", "MultiAssayExperiment", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VGAM", "data_table", "formula_tools", "ggplot2", "gtools", "memoise", "plyr", "reshape2", "rlang", "rtracklayer", "scales", "som", "stringdist", "stringi", "vegan"] 821 }, 822 "CAMERA": { 823 "name": "CAMERA", 824 "version": "1.66.0", 825 "sha256": "1sxdpnwyy2ai4f4za5dh9hlksz772a4cc86qjzm24f7j27hw44zm", 826 "depends": ["Biobase", "Hmisc", "RBGL", "graph", "igraph", "xcms"] 827 }, 828 "CARDspa": { 829 "name": "CARDspa", 830 "version": "1.2.0", 831 "sha256": "04n4pffqrpgf57crdg3pg0av510y73fkwm6irsvy1kdj183585vv", 832 "depends": ["BiocParallel", "MCMCpack", "Matrix", "NMF", "RANN", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppML", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "concaveman", "dplyr", "fields", "ggcorrplot", "ggplot2", "gtools", "nnls", "reshape2", "scatterpie", "sf", "sp", "spatstat_random", "wrMisc"] 833 }, 834 "CARNIVAL": { 835 "name": "CARNIVAL", 836 "version": "2.20.0", 837 "sha256": "1d9nbns330mgi4nkzfvvaxg50lafmf3nd93lrwflsi8mb9p1pjp3", 838 "depends": ["dplyr", "igraph", "lpSolve", "readr", "rjson", "rmarkdown", "stringr", "tibble", "tidyr"] 839 }, 840 "CATALYST": { 841 "name": "CATALYST", 842 "version": "1.34.0", 843 "sha256": "0fp0sg010kb7nq2c1v68rw94z5l62vq6wql3w8690baivrp1crj7", 844 "depends": ["ComplexHeatmap", "ConsensusClusterPlus", "FlowSOM", "Matrix", "RColorBrewer", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "cowplot", "data_table", "dplyr", "drc", "flowCore", "ggplot2", "ggrepel", "ggridges", "gridExtra", "matrixStats", "nnls", "purrr", "reshape2", "scales", "scater"] 845 }, 846 "CBN2Path": { 847 "name": "CBN2Path", 848 "version": "0.99.18", 849 "sha256": "03sa6j6mbf16gd9zwv4j6hbv8gd2la67h2vk6qmww49rikijmmx4", 850 "depends": ["BiocParallel", "R6", "TCGAbiolinks", "coda", "cowplot", "ggplot2", "ggraph", "igraph", "magrittr", "patchwork", "rlang", "tidygraph"] 851 }, 852 "CBNplot": { 853 "name": "CBNplot", 854 "version": "1.10.0", 855 "sha256": "169kj6snwb678q9y253bk3xx6ysv55plmrmf5rc2qhq7a0acarbf", 856 "depends": ["BiocFileCache", "ExperimentHub", "Rmpfr", "bnlearn", "clusterProfiler", "depmap", "dplyr", "enrichplot", "ggdist", "ggforce", "ggplot2", "ggraph", "graphite", "graphlayouts", "igraph", "magrittr", "org_Hs_eg_db", "patchwork", "purrr", "pvclust", "reshape2", "rlang", "stringr", "tidyr"] 857 }, 858 "CCAFE": { 859 "name": "CCAFE", 860 "version": "1.2.0", 861 "sha256": "1f8b2ay5dmpkyhwik0wks4k3mbqa97p5akwdycggprrgknmk24yw", 862 "depends": ["VariantAnnotation", "dplyr"] 863 }, 864 "CCPROMISE": { 865 "name": "CCPROMISE", 866 "version": "1.36.0", 867 "sha256": "1qbmkmg5hyxrk5dsb33yax47f82b1j9sq1rmg5z9zq5jmy8d5lab", 868 "depends": ["Biobase", "CCP", "GSEABase", "PROMISE"] 869 }, 870 "CCPlotR": { 871 "name": "CCPlotR", 872 "version": "1.8.0", 873 "sha256": "1a6pkyl36g5wi8f14hnyn8x97vclmh84l3dcy6gd5h9vddy9kbhg", 874 "depends": ["ComplexHeatmap", "RColorBrewer", "circlize", "dplyr", "forcats", "ggbump", "ggh4x", "ggplot2", "ggraph", "ggtext", "igraph", "patchwork", "plyr", "scales", "scatterpie", "stringr", "tibble", "tidyr", "viridis"] 875 }, 876 "CDI": { 877 "name": "CDI", 878 "version": "1.8.0", 879 "sha256": "1k5sxbbmcvb4widaf1r9fzlrhx6q6gqlpiy7lcfrhkhg8l8k2xz6", 880 "depends": ["BiocParallel", "Seurat", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggsci", "matrixStats", "reshape2"] 881 }, 882 "CEMiTool": { 883 "name": "CEMiTool", 884 "version": "1.34.0", 885 "sha256": "0lbql9dmriz2lpvynbl2yw24mi2acipqq2wmz40rha9jqjdq8lq8", 886 "depends": ["DT", "WGCNA", "clusterProfiler", "data_table", "dplyr", "fastcluster", "fgsea", "ggdendro", "ggplot2", "ggpmisc", "ggrepel", "ggthemes", "gridExtra", "gtable", "htmltools", "igraph", "intergraph", "knitr", "matrixStats", "network", "pracma", "rmarkdown", "scales", "sna", "stringr"] 887 }, 888 "CFAssay": { 889 "name": "CFAssay", 890 "version": "1.44.0", 891 "sha256": "0m8p932rzlnnh6wa9d05y9pn1h6zzgv97qkg25xhcfwk98jb3qhj", 892 "depends": [] 893 }, 894 "CGEN": { 895 "name": "CGEN", 896 "version": "3.46.0", 897 "sha256": "01a6qhrib1d0xv56s2ns4p76zgvq38dsivz6z1l0dqgnjq593br0", 898 "depends": ["mvtnorm", "survival"] 899 }, 900 "CGHbase": { 901 "name": "CGHbase", 902 "version": "1.70.0", 903 "sha256": "0hkbm2q24qaga6py5gvdcirrb0paspdb9s7nkvgi7fdrdw8r7lg0", 904 "depends": ["Biobase", "marray"] 905 }, 906 "CGHcall": { 907 "name": "CGHcall", 908 "version": "2.72.0", 909 "sha256": "0wb3fmr8f2cdfbq2a3bdpk3v5fwsvr5632k4dsyi9zi33lr0l9zc", 910 "depends": ["Biobase", "CGHbase", "DNAcopy", "impute", "snowfall"] 911 }, 912 "CGHnormaliter": { 913 "name": "CGHnormaliter", 914 "version": "1.64.0", 915 "sha256": "0rbbffmfs0a4my9lfha2wicyj37hyxyhz2f5z1x71brfgyl2gc8l", 916 "depends": ["Biobase", "CGHbase", "CGHcall"] 917 }, 918 "CGHregions": { 919 "name": "CGHregions", 920 "version": "1.68.0", 921 "sha256": "1rsr876426ncc12x021z2ll17indvxh82w8dflljiwshbw5fyvqi", 922 "depends": ["Biobase", "CGHbase"] 923 }, 924 "CHETAH": { 925 "name": "CHETAH", 926 "version": "1.26.0", 927 "sha256": "0nk99mc25ylxl6mzmswswwhyjd1cd4g4mvw8mk2y0anhlldzma83", 928 "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bioDist", "corrplot", "cowplot", "dendextend", "ggplot2", "pheatmap", "plotly", "reshape2", "shiny"] 929 }, 930 "CHRONOS": { 931 "name": "CHRONOS", 932 "version": "1.38.0", 933 "sha256": "0gkwwx2ka5rn7yl068iy7q5cs3xidyhpy3jja1xx27ri5blql290", 934 "depends": ["RBGL", "RCurl", "XML", "biomaRt", "circlize", "doParallel", "foreach", "graph", "igraph", "openxlsx", "rJava"] 935 }, 936 "CIMICE": { 937 "name": "CIMICE", 938 "version": "1.18.0", 939 "sha256": "10nl1dgvp93vgrgib49n3v4jr8jpl8xgc02gf4zr8s5gbsjrd820", 940 "depends": ["Matrix", "assertthat", "dplyr", "expm", "ggcorrplot", "ggplot2", "ggraph", "glue", "igraph", "maftools", "networkD3", "purrr", "tidygraph", "tidyr", "visNetwork"] 941 }, 942 "CMA": { 943 "name": "CMA", 944 "version": "1.68.0", 945 "sha256": "0z62z9a1jvddddkqxsajllldadgwcp6ir5h12adb0wys9v2v8h4m", 946 "depends": ["Biobase"] 947 }, 948 "CNAnorm": { 949 "name": "CNAnorm", 950 "version": "1.56.0", 951 "sha256": "1jkq0ryv2s7r693y75c1l7dy8p2r9mq9yh369ibv0ybj8r0fa18b", 952 "depends": ["DNAcopy"] 953 }, 954 "CNEr": { 955 "name": "CNEr", 956 "version": "1.46.0", 957 "sha256": "18ii60kxr3f1rsydj29ml49gjicnciq7ypvrm1dz2rv4app0bp5j", 958 "depends": ["BiocGenerics", "Biostrings", "DBI", "GO_db", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "KEGGREST", "RSQLite", "R_utils", "S4Vectors", "Seqinfo", "XVector", "annotate", "ggplot2", "poweRlaw", "pwalign", "readr", "reshape2", "rtracklayer"] 959 }, 960 "CNORdt": { 961 "name": "CNORdt", 962 "version": "1.52.0", 963 "sha256": "1237z0l800dh45dvj02v2mys9mhh3pg0as760l3lvn95vf0shbj1", 964 "depends": ["CellNOptR", "abind"] 965 }, 966 "CNORfeeder": { 967 "name": "CNORfeeder", 968 "version": "1.50.0", 969 "sha256": "1xfymy60fadhzphyin8n5f035c3sj8rd9xcwyas2r1q53nyliwmz", 970 "depends": ["CellNOptR", "graph"] 971 }, 972 "CNORfuzzy": { 973 "name": "CNORfuzzy", 974 "version": "1.52.0", 975 "sha256": "0fcda4rmx278i60kgcj0rk70nrf5rqq3sa5b0fn8dqj28p879slb", 976 "depends": ["CellNOptR", "nloptr"] 977 }, 978 "CNORode": { 979 "name": "CNORode", 980 "version": "1.52.0", 981 "sha256": "1dma5y9bwidkwr29379iahs41hb6gfczhsx6qncivmp7f62fs49v", 982 "depends": ["CellNOptR", "genalg"] 983 }, 984 "CNTools": { 985 "name": "CNTools", 986 "version": "1.66.0", 987 "sha256": "0ya5l1hijqyknzxspdyahnnrrkfl9li54apzhay4lx6qcim7r7dy", 988 "depends": ["genefilter"] 989 }, 990 "CNVMetrics": { 991 "name": "CNVMetrics", 992 "version": "1.13.0", 993 "sha256": "0pvlc1blwqar2agnl3hdm467x162n8i3sb6kpzqsr2xw44zvx2w2", 994 "depends": ["BiocParallel", "GenomicRanges", "IRanges", "S4Vectors", "gridExtra", "magrittr", "pheatmap", "rBeta2009"] 995 }, 996 "CNVPanelizer": { 997 "name": "CNVPanelizer", 998 "version": "1.42.0", 999 "sha256": "19f3cipi5srwhm33mf12l3840da7dvbpj3yaw1vb1ljhq076fq23", 1000 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "NOISeq", "Rsamtools", "S4Vectors", "foreach", "ggplot2", "gplots", "openxlsx", "plyr", "reshape2", "shiny", "shinyFiles", "shinyjs", "stringr", "testthat"] 1001 }, 1002 "CNVRanger": { 1003 "name": "CNVRanger", 1004 "version": "1.26.0", 1005 "sha256": "0ajca3q7ij72wvdhjv3yb2dxz014ivhsrkdq8zil6hkdcg0afzhi", 1006 "depends": ["BiocGenerics", "BiocParallel", "GDSArray", "GenomeInfoDb", "GenomicRanges", "IRanges", "RaggedExperiment", "S4Vectors", "SNPRelate", "SummarizedExperiment", "data_table", "edgeR", "gdsfmt", "lattice", "limma", "plyr", "qqman", "rappdirs", "reshape2"] 1007 }, 1008 "CNVfilteR": { 1009 "name": "CNVfilteR", 1010 "version": "1.24.0", 1011 "sha256": "0qgd3fyy49yqh13nz1vgqsmwrqsfx5as42ydp2qz6qgzj01j781g", 1012 "depends": ["Biostrings", "CopyNumberPlots", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation", "assertthat", "karyoploteR", "pracma", "regioneR"] 1013 }, 1014 "CNViz": { 1015 "name": "CNViz", 1016 "version": "1.18.0", 1017 "sha256": "0f6ah1qvncb87wb6x0jngjh3r6b1ipy8g0hik5hvq6gmwy4n53is", 1018 "depends": ["CopyNumberPlots", "DT", "GenomicRanges", "dplyr", "karyoploteR", "magrittr", "plotly", "scales", "shiny"] 1019 }, 1020 "CNVrd2": { 1021 "name": "CNVrd2", 1022 "version": "1.48.0", 1023 "sha256": "120bm81m58b08y4wkk1wqb58xsiqn7jf8adyvga5kjx2gfav61rp", 1024 "depends": ["DNAcopy", "IRanges", "Rsamtools", "VariantAnnotation", "ggplot2", "gridExtra", "rjags"] 1025 }, 1026 "COCOA": { 1027 "name": "COCOA", 1028 "version": "2.24.0", 1029 "sha256": "00iwq26f4gjcim4ia0lqsz1mpakifvh2za23s2ds7033r4barg4j", 1030 "depends": ["Biobase", "BiocGenerics", "ComplexHeatmap", "GenomicRanges", "IRanges", "MIRA", "S4Vectors", "data_table", "fitdistrplus", "ggplot2", "simpleCache", "tidyr"] 1031 }, 1032 "CODEX": { 1033 "name": "CODEX", 1034 "version": "1.42.0", 1035 "sha256": "09di6yq4m6p7hzk6gasavgf1h91160apac6w5wp1qzl7rjxkw443", 1036 "depends": ["BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "GenomeInfoDb", "IRanges", "Rsamtools", "S4Vectors"] 1037 }, 1038 "COMPASS": { 1039 "name": "COMPASS", 1040 "version": "1.48.0", 1041 "sha256": "0w20swwqanphskmb1ds2yby16ynxy4br443504bwm1bk830piqmi", 1042 "depends": ["BiocStyle", "RColorBrewer", "Rcpp", "abind", "clue", "coda", "data_table", "dplyr", "foreach", "knitr", "magrittr", "pdist", "plyr", "reshape2", "rlang", "rmarkdown", "scales", "tidyr"] 1043 }, 1044 "CONFESS": { 1045 "name": "CONFESS", 1046 "version": "1.38.0", 1047 "sha256": "1nwsm4hmyndnkqi8xwhr1z7vfysds2v2j0mm37ip1r6sc2l87gln", 1048 "depends": ["EBImage", "MASS", "SamSPECTRAL", "changepoint", "cluster", "contrast", "data_table", "ecp", "flexmix", "flowClust", "flowCore", "flowMeans", "flowMerge", "flowPeaks", "foreach", "ggplot2", "limma", "moments", "outliers", "plotrix", "raster", "readbitmap", "reshape2", "waveslim", "wavethresh", "zoo"] 1049 }, 1050 "CONSTANd": { 1051 "name": "CONSTANd", 1052 "version": "1.18.0", 1053 "sha256": "0i25ggwn69dk34iwaa8krpba81g15k8f6aj31jzmv8j2x0fgbx8v", 1054 "depends": [] 1055 }, 1056 "COSNet": { 1057 "name": "COSNet", 1058 "version": "1.44.0", 1059 "sha256": "07ipxvl880kh0wcplq68yaimzijzss7q34f999a0h76zynr6736n", 1060 "depends": [] 1061 }, 1062 "COTAN": { 1063 "name": "COTAN", 1064 "version": "2.10.0", 1065 "sha256": "0msq2ij3ppyzpsbc7ziyrhgwpxw3a91bncb4xg3bzz1w396q0hq4", 1066 "depends": ["BiocSingular", "ComplexHeatmap", "Matrix", "RColorBrewer", "RSpectra", "Rfast", "Seurat", "SingleCellExperiment", "assertthat", "circlize", "dendextend", "dplyr", "gghalves", "ggplot2", "ggrepel", "ggthemes", "parallelDist", "parallelly", "proxy", "rlang", "scales", "stringr", "tibble", "tidyr", "withr", "zeallot"] 1067 }, 1068 "CPSM": { 1069 "name": "CPSM", 1070 "version": "1.2.0", 1071 "sha256": "0a191x65v5vhyzcf16flqa7rs6xjq3ds6icv2r0263cjn0y21hiy", 1072 "depends": ["Hmisc", "MASS", "MTLR", "Matrix", "SummarizedExperiment", "SurvMetrics", "caret", "ggfortify", "ggplot2", "glmnet", "preprocessCore", "randomForestSRC", "reshape2", "rms", "survival", "survminer"] 1073 }, 1074 "CRISPRseek": { 1075 "name": "CRISPRseek", 1076 "version": "1.50.0", 1077 "sha256": "1248b7jniz2d2cj3srrqfx0aaga42g9pymbhawwjcaasknyb83lp", 1078 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "DelayedArray", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "XVector", "data_table", "dplyr", "gtools", "hash", "keras", "mltools", "openxlsx", "reticulate", "rhdf5", "rio", "rlang", "seqinr", "stringr"] 1079 }, 1080 "CRImage": { 1081 "name": "CRImage", 1082 "version": "1.58.0", 1083 "sha256": "19yafswp9j5s0k1wd8891vlkqjgj7249mh075qg8gjaxknc0x7q2", 1084 "depends": ["DNAcopy", "EBImage", "MASS", "aCGH", "e1071", "foreach", "sgeostat"] 1085 }, 1086 "CSAR": { 1087 "name": "CSAR", 1088 "version": "1.62.0", 1089 "sha256": "0bi6iav4255bvbidi1cy6k1dnvijypy8ypxd2kg6sfcgsz8pgir6", 1090 "depends": ["GenomicRanges", "IRanges", "S4Vectors", "Seqinfo"] 1091 }, 1092 "CSOA": { 1093 "name": "CSOA", 1094 "version": "1.0.0", 1095 "sha256": "0rs8qn6i55xhf5ci19yihc4wdq51zyav1zx5ax1z6ivd5v0jhv9g", 1096 "depends": ["Seurat", "SeuratObject", "SummarizedExperiment", "bayesbio", "dplyr", "ggplot2", "henna", "kerntools", "qs", "reshape2", "rlang", "sgof", "spatstat_utils", "textshape", "wesanderson"] 1097 }, 1098 "CSSQ": { 1099 "name": "CSSQ", 1100 "version": "1.22.0", 1101 "sha256": "15nn72g3a1ji4fla29s5jdwy8ihswg1gv9vjc2cglxlixisrj9jq", 1102 "depends": ["GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "ggplot2", "rtracklayer"] 1103 }, 1104 "CTDquerier": { 1105 "name": "CTDquerier", 1106 "version": "2.18.0", 1107 "sha256": "0rf6qf6ycxn183njf7qj94rj7g5m9p44c5wyysn6fkw3yxlvqq3a", 1108 "depends": ["BiocFileCache", "RCurl", "S4Vectors", "ggplot2", "gridExtra", "igraph", "stringdist", "stringr"] 1109 }, 1110 "CTSV": { 1111 "name": "CTSV", 1112 "version": "1.12.0", 1113 "sha256": "10df3fd2jj29sf05p36l6aswibqhfi9x6sa6ql7z0zhhr3frprjv", 1114 "depends": ["BiocParallel", "SpatialExperiment", "SummarizedExperiment", "knitr", "pscl", "qvalue"] 1115 }, 1116 "CTdata": { 1117 "name": "CTdata", 1118 "version": "1.10.0", 1119 "sha256": "0izpgr94hqha38aik6dvip6wbrzynyqwpms403sd6f0vcm559k51", 1120 "depends": ["ExperimentHub"] 1121 }, 1122 "CTexploreR": { 1123 "name": "CTexploreR", 1124 "version": "1.6.0", 1125 "sha256": "0c5x958gg18lm6q9g7i32p13ng3y0z1lpgds3mpsj58lv2iavpn8", 1126 "depends": ["BiocGenerics", "CTdata", "ComplexHeatmap", "GenomicRanges", "IRanges", "MatrixGenerics", "SingleCellExperiment", "SummarizedExperiment", "circlize", "dplyr", "ggplot2", "ggrepel", "rlang", "tibble", "tidyr"] 1127 }, 1128 "CaDrA": { 1129 "name": "CaDrA", 1130 "version": "1.8.0", 1131 "sha256": "0x3d5qam54x177qbk0z2qdylb2kx93hb6616z5148bjn2bnwlhy3", 1132 "depends": ["MASS", "R_cache", "SummarizedExperiment", "doParallel", "ggplot2", "gplots", "gtable", "knnmi", "misc3d", "plyr", "ppcor", "reshape2"] 1133 }, 1134 "CaMutQC": { 1135 "name": "CaMutQC", 1136 "version": "1.6.0", 1137 "sha256": "13j264akf38aln2kc3899yj7r77fs255vhp2hb2zm2h0fxm006ry", 1138 "depends": ["DT", "MesKit", "clusterProfiler", "data_table", "dplyr", "ggplot2", "maftools", "org_Hs_eg_db", "stringr", "tidyr", "vcfR"] 1139 }, 1140 "CalibraCurve": { 1141 "name": "CalibraCurve", 1142 "version": "1.0.0", 1143 "sha256": "0x73svnc2h6ib43zagq0qaavqv16zp26gg7hd9525mfkxcbhpqrv", 1144 "depends": ["SummarizedExperiment", "checkmate", "dplyr", "ggplot2", "magrittr", "openxlsx", "scales", "tidyr"] 1145 }, 1146 "Cardinal": { 1147 "name": "Cardinal", 1148 "version": "3.12.0", 1149 "sha256": "0399hpf81s5hfd2yrq62md29p7y1f55wqb6kn9n3kg6i1z12qdpn", 1150 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "CardinalIO", "EBImage", "Matrix", "ProtGenerics", "S4Vectors", "irlba", "matter", "nlme"] 1151 }, 1152 "CardinalIO": { 1153 "name": "CardinalIO", 1154 "version": "1.8.0", 1155 "sha256": "1qfb61gbrjq05dd53smdvk04gcgvr15jkpnkcjydl2g12sdnxfnp", 1156 "depends": ["BiocParallel", "S4Vectors", "matter", "ontologyIndex"] 1157 }, 1158 "Category": { 1159 "name": "Category", 1160 "version": "2.76.0", 1161 "sha256": "1awaxnmnzs260pl2lzvmbhds17347kjln11iwbpabisyrvx8gzb2", 1162 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "GSEABase", "Matrix", "RBGL", "annotate", "genefilter", "graph"] 1163 }, 1164 "CatsCradle": { 1165 "name": "CatsCradle", 1166 "version": "1.3.3", 1167 "sha256": "1rrwxjscma49bmhpyx8gv4lgqyrngqzk77phbryajpmagw81mfwl", 1168 "depends": ["EBImage", "Matrix", "Rfast", "S4Vectors", "Seurat", "SeuratObject", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "abind", "data_table", "geometry", "ggplot2", "igraph", "msigdbr", "networkD3", "pheatmap", "pracma", "rdist", "reshape2", "stringr"] 1169 }, 1170 "CausalR": { 1171 "name": "CausalR", 1172 "version": "1.42.0", 1173 "sha256": "0h4p9ml4kv0wbphs9whbyq18yakq8wlwkvac1kg5q6ym43v8w2zw", 1174 "depends": ["igraph"] 1175 }, 1176 "CeTF": { 1177 "name": "CeTF", 1178 "version": "1.22.0", 1179 "sha256": "0ri9kkx8iysz54iq79r3ngmgw0zhwl9svw82l5a67jjd74wwai1l", 1180 "depends": ["ComplexHeatmap", "DESeq2", "GGally", "GenomicTools_fileHandler", "Matrix", "RCy3", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "circlize", "clusterProfiler", "dplyr", "ggnetwork", "ggplot2", "ggpubr", "ggrepel", "igraph", "network"] 1181 }, 1182 "CellBarcode": { 1183 "name": "CellBarcode", 1184 "version": "1.16.0", 1185 "sha256": "033ysn8kins6w66nkl6m5spc65g1k1bi08adnp69jz2ygr0drf5y", 1186 "depends": ["BH", "Biostrings", "Ckmeans_1d_dp", "Rcpp", "Rsamtools", "S4Vectors", "ShortRead", "data_table", "egg", "ggplot2", "magrittr", "plyr", "seqinr", "stringr"] 1187 }, 1188 "CellBench": { 1189 "name": "CellBench", 1190 "version": "1.26.0", 1191 "sha256": "0zqa72c2g92ibzy5wgpj5g4g6vnfsg0jk1j49avbh0jrmhkxk4jw", 1192 "depends": ["BiocFileCache", "BiocGenerics", "BiocParallel", "SingleCellExperiment", "assertthat", "dplyr", "glue", "lubridate", "magrittr", "memoise", "purrr", "rappdirs", "rlang", "tibble", "tidyr", "tidyselect"] 1193 }, 1194 "CellMapper": { 1195 "name": "CellMapper", 1196 "version": "1.36.0", 1197 "sha256": "0vrwxiqbrn1ij1kr17ppzgb22livf78x1j8sj6shv7g5as09mabk", 1198 "depends": ["S4Vectors"] 1199 }, 1200 "CellMixS": { 1201 "name": "CellMixS", 1202 "version": "1.26.0", 1203 "sha256": "1asdsy8i9wlwnxjfkvxa28n2sdkphd5qn0v7lkhj7vk9nh0f4zf2", 1204 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "SingleCellExperiment", "SummarizedExperiment", "cowplot", "dplyr", "ggplot2", "ggridges", "kSamples", "magrittr", "purrr", "scater", "tidyr", "viridis"] 1205 }, 1206 "CellNOptR": { 1207 "name": "CellNOptR", 1208 "version": "1.56.0", 1209 "sha256": "0p4jj80qhll4ih0mxz32f2s29cfxmwcxd2ipsb6rr0081c3jbiwi", 1210 "depends": ["RBGL", "RCurl", "Rgraphviz", "XML", "ggplot2", "graph", "igraph", "rmarkdown", "stringi", "stringr"] 1211 }, 1212 "CellTrails": { 1213 "name": "CellTrails", 1214 "version": "1.28.0", 1215 "sha256": "0ssyb5qfnbcippqj2d9y9lvnimqicmzb4rhfhpxhi2rflra5rlp6", 1216 "depends": ["Biobase", "BiocGenerics", "EnvStats", "Rtsne", "SingleCellExperiment", "SummarizedExperiment", "cba", "dendextend", "dtw", "ggplot2", "ggrepel", "igraph", "maptree", "mgcv", "reshape2"] 1217 }, 1218 "CelliD": { 1219 "name": "CelliD", 1220 "version": "1.18.0", 1221 "sha256": "1bvj7n2qxfvy1fmjqmm1w65fcj7fy5h74i0jgl0a0940mlhd7s9v", 1222 "depends": ["BiocParallel", "Matrix", "Rcpp", "RcppArmadillo", "Rtsne", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "data_table", "fastmatch", "fgsea", "ggplot2", "glue", "irlba", "matrixStats", "pbapply", "reticulate", "scater", "stringr", "tictoc", "umap"] 1223 }, 1224 "Cepo": { 1225 "name": "Cepo", 1226 "version": "1.16.0", 1227 "sha256": "0j3z7pycc30zk1j2b7skk2jav4z9cp6n1qhzn9gji6qzxkzrzpyb", 1228 "depends": ["BiocParallel", "DelayedArray", "DelayedMatrixStats", "GSEABase", "HDF5Array", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "patchwork", "purrr", "reshape2", "rlang"] 1229 }, 1230 "CexoR": { 1231 "name": "CexoR", 1232 "version": "1.48.0", 1233 "sha256": "1ah5564xyxm2c1rg5qircsz7cg3wil3q4kmxmvwc2nw867pdzhk4", 1234 "depends": ["GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "genomation", "idr", "rtracklayer"] 1235 }, 1236 "ChAMP": { 1237 "name": "ChAMP", 1238 "version": "2.40.0", 1239 "sha256": "151q3702xfll347y9yfbslcagd6idagk69jv69vd3yqzwacg58w2", 1240 "depends": ["ChAMPdata", "DMRcate", "DNAcopy", "DT", "GenomicRanges", "Hmisc", "Illumina450ProbeVariants_db", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno_ilm10b4_hg19", "IlluminaHumanMethylationEPICmanifest", "RColorBrewer", "RPMM", "bumphunter", "combinat", "dendextend", "doParallel", "ggplot2", "globaltest", "goseq", "illuminaio", "impute", "isva", "limma", "marray", "matrixStats", "minfi", "missMethyl", "plotly", "plyr", "preprocessCore", "prettydoc", "quadprog", "qvalue", "rmarkdown", "shiny", "shinythemes", "sva", "wateRmelon"] 1241 }, 1242 "ChIPComp": { 1243 "name": "ChIPComp", 1244 "version": "1.40.0", 1245 "sha256": "0mbsrq97bfi3fpf2lyq1q2bqrhl1y2klk6x2ydvph2m0k3zbhp5n", 1246 "depends": ["BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Mmusculus_UCSC_mm9", "BiocGenerics", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "limma", "rtracklayer"] 1247 }, 1248 "ChIPXpress": { 1249 "name": "ChIPXpress", 1250 "version": "1.54.0", 1251 "sha256": "1rpn1c07by5zjkh2nnm5jrcz81ixp6zmhfj51a13hcz1bsa4as16", 1252 "depends": ["Biobase", "ChIPXpressData", "GEOquery", "affy", "biganalytics", "bigmemory", "frma"] 1253 }, 1254 "ChIPanalyser": { 1255 "name": "ChIPanalyser", 1256 "version": "1.32.0", 1257 "sha256": "1sd9wcdn4miawyyp5z5q2xqjvzhgjpahdbha9fgpgbnlx8qq7yvg", 1258 "depends": ["BSgenome", "BiocManager", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "ROCR", "RcppRoll", "S4Vectors", "rtracklayer"] 1259 }, 1260 "ChIPexoQual": { 1261 "name": "ChIPexoQual", 1262 "version": "1.34.0", 1263 "sha256": "1z72y7jfl1gmcgkkrjqjhj8cq8c224llrdihgrr2zj2k7nsqhnkd", 1264 "depends": ["BiocParallel", "GenomicAlignments", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "biovizBase", "broom", "data_table", "dplyr", "ggplot2", "hexbin", "rmarkdown", "scales", "viridis"] 1265 }, 1266 "ChIPpeakAnno": { 1267 "name": "ChIPpeakAnno", 1268 "version": "3.44.0", 1269 "sha256": "0i3iw6wafpwb2l99ay306wdafjb25wwpjvrggq515vibz7zvrxh2", 1270 "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "InteractionSet", "KEGGREST", "RBGL", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VennDiagram", "biomaRt", "data_table", "dplyr", "ensembldb", "ggplot2", "graph", "matrixStats", "multtest", "pwalign", "regioneR", "rtracklayer", "scales", "stringr", "tibble", "tidyr", "universalmotif"] 1271 }, 1272 "ChIPseeker": { 1273 "name": "ChIPseeker", 1274 "version": "1.45.0", 1275 "sha256": "1rq9jj7gs3g2dvzpglhydiyd76l4i12kc47l9gl7lcvnwpvpkbn8", 1276 "depends": ["AnnotationDbi", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "aplot", "boot", "dplyr", "enrichplot", "ggplot2", "gplots", "gtools", "magrittr", "plotrix", "rlang", "rtracklayer", "scales", "tibble", "yulab_utils"] 1277 }, 1278 "ChIPseqR": { 1279 "name": "ChIPseqR", 1280 "version": "1.64.0", 1281 "sha256": "0zzmxaiz3n025qicf1vj4xlnz05xa8d0iahk6s3pvc91az4r35jc", 1282 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "HilbertVis", "IRanges", "S4Vectors", "ShortRead", "fBasics", "timsac"] 1283 }, 1284 "ChIPsim": { 1285 "name": "ChIPsim", 1286 "version": "1.64.0", 1287 "sha256": "0f3lvdn44njfk5172ds0g6zk0hcmx41mkhyz34gisbxm5w0ba578", 1288 "depends": ["Biostrings", "IRanges", "ShortRead", "XVector"] 1289 }, 1290 "ChemmineOB": { 1291 "name": "ChemmineOB", 1292 "version": "1.48.0", 1293 "sha256": "03pw3758my4j5d94kg3vklqy6nmp2aw664d55kwd6ww21xi0b0ln", 1294 "depends": ["BH", "BiocGenerics", "Rcpp"] 1295 }, 1296 "ChemmineR": { 1297 "name": "ChemmineR", 1298 "version": "3.62.0", 1299 "sha256": "0yvf72nz3s151hsclwk8ch0rypsm7a4z3w49ds7rnqd92q1h0rx5", 1300 "depends": ["BH", "BiocGenerics", "DBI", "DT", "RCurl", "Rcpp", "base64enc", "digest", "ggplot2", "gridExtra", "jsonlite", "png", "rjson", "rsvg", "stringi"] 1301 }, 1302 "Chicago": { 1303 "name": "Chicago", 1304 "version": "1.38.0", 1305 "sha256": "1bmc7b6fgq5bw9msp4snycvw00r4wxasax9li92zsw3kva9ys941", 1306 "depends": ["Delaporte", "Hmisc", "MASS", "data_table", "matrixStats"] 1307 }, 1308 "ChromHeatMap": { 1309 "name": "ChromHeatMap", 1310 "version": "1.64.0", 1311 "sha256": "0v499mfdhhbf9yspaayk6pdzarspjsdgj3swnfw8zwd1qiazbidp", 1312 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "annotate", "rtracklayer"] 1313 }, 1314 "ChromSCape": { 1315 "name": "ChromSCape", 1316 "version": "1.20.0", 1317 "sha256": "103qfjjdzbi7nn3qlz28rm88p1qlphd98dqwmpr3fffg864kg885", 1318 "depends": ["BiocParallel", "ConsensusClusterPlus", "DT", "DelayedArray", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "Rsamtools", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "batchelor", "colorRamps", "colourpicker", "coop", "dplyr", "edgeR", "forcats", "fs", "gggenes", "ggplot2", "ggrepel", "gridExtra", "irlba", "jsonlite", "kableExtra", "matrixTests", "msigdbr", "plotly", "qs", "qualV", "rlist", "rtracklayer", "scater", "scran", "shiny", "shinyFiles", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinydashboardPlus", "shinyhelper", "shinyjs", "stringdist", "stringr", "tibble", "tidyr", "umap", "viridis"] 1319 }, 1320 "Chromatograms": { 1321 "name": "Chromatograms", 1322 "version": "1.0.0", 1323 "sha256": "1kam7kxcldag928m97zdp9665lg5ypd9nlamzz1hdamhd0ayqkg2", 1324 "depends": ["BiocParallel", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra"] 1325 }, 1326 "CircSeqAlignTk": { 1327 "name": "CircSeqAlignTk", 1328 "version": "1.12.0", 1329 "sha256": "0494hwvdip55c44vkwr5a2y2nmv5q1r4nk2c6fdwrwc2wc4lg6jb", 1330 "depends": ["BiocGenerics", "Biostrings", "IRanges", "R_utils", "Rbowtie2", "Rhisat2", "Rsamtools", "S4Vectors", "ShortRead", "dplyr", "ggplot2", "htmltools", "magrittr", "plotly", "rlang", "shiny", "shinyFiles", "shinyjs", "tidyr"] 1331 }, 1332 "CiteFuse": { 1333 "name": "CiteFuse", 1334 "version": "1.22.0", 1335 "sha256": "1s51ch8j0p7h2g13db0g1mcrg1kixby0jg75nx21aa55rjj1qrw7", 1336 "depends": ["Matrix", "Rcpp", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "compositions", "cowplot", "dbscan", "ggplot2", "ggraph", "ggridges", "gridExtra", "igraph", "mixtools", "pheatmap", "randomForest", "reshape2", "rhdf5", "rlang", "scales", "scran", "uwot"] 1337 }, 1338 "ClassifyR": { 1339 "name": "ClassifyR", 1340 "version": "3.14.0", 1341 "sha256": "1bxvd5nwjk3i3n6ygp11j22451gcsjq91vc118fp4sc7vk4fpabw", 1342 "depends": ["BiocParallel", "MultiAssayExperiment", "S4Vectors", "broom", "dcanr", "dplyr", "genefilter", "generics", "ggplot2", "ggpubr", "ggupset", "ranger", "reshape2", "rlang", "survival", "tidyr"] 1343 }, 1344 "CleanUpRNAseq": { 1345 "name": "CleanUpRNAseq", 1346 "version": "1.4.0", 1347 "sha256": "0iz4rcbasg9ji5n074imsq2inwwr6vndr6hn94954cz2c7g73qsx", 1348 "depends": ["AnnotationFilter", "BSgenome", "BiocGenerics", "Biostrings", "DESeq2", "GenomicRanges", "KernSmooth", "R6", "RColorBrewer", "Rsamtools", "Rsubread", "Seqinfo", "SummarizedExperiment", "edgeR", "ensembldb", "ggplot2", "ggrepel", "limma", "pheatmap", "qsmooth", "reshape2", "tximport"] 1349 }, 1350 "Clomial": { 1351 "name": "Clomial", 1352 "version": "1.46.0", 1353 "sha256": "0mkbfnj05pj5qfk5zc3zdyh32pm1arq1rv6yg4dp3mabh156w01z", 1354 "depends": ["matrixStats", "permute"] 1355 }, 1356 "CluMSID": { 1357 "name": "CluMSID", 1358 "version": "1.26.0", 1359 "sha256": "15a4j5374cy5zw52h643csmwkcd9i6826ilm6sabm1hgq1134gmp", 1360 "depends": ["Biobase", "GGally", "MSnbase", "RColorBrewer", "S4Vectors", "ape", "dbscan", "ggplot2", "gplots", "mzR", "network", "plotly", "sna"] 1361 }, 1362 "ClustAll": { 1363 "name": "ClustAll", 1364 "version": "1.6.0", 1365 "sha256": "1rvyrqdyg6qmi18qbv9mzhq1rdr24kbm9aizgrw67j9znmz70mxs", 1366 "depends": ["ComplexHeatmap", "FactoMineR", "RColorBrewer", "bigstatsr", "circlize", "clValid", "cluster", "doSNOW", "dplyr", "flock", "foreach", "fpc", "ggplot2", "mice", "modeest", "networkD3", "pbapply"] 1367 }, 1368 "ClustIRR": { 1369 "name": "ClustIRR", 1370 "version": "1.8.0", 1371 "sha256": "1lk074kvgfxj6bwqv6jmbgx3nphh07sj5hlcpvy8695j9sjmjn5s", 1372 "depends": ["BH", "Rcpp", "RcppEigen", "RcppParallel", "StanHeaders", "blaster", "dplyr", "future", "future_apply", "ggforce", "ggplot2", "igraph", "posterior", "reshape2", "rstan", "rstantools", "scales", "stringdist", "tidyr", "visNetwork"] 1373 }, 1374 "ClusterFoldSimilarity": { 1375 "name": "ClusterFoldSimilarity", 1376 "version": "1.6.0", 1377 "sha256": "08jhfqr7llnrm9b673vclnd9xqn37jzbmml0p5w7bqcvk4jy6cls", 1378 "depends": ["BiocParallel", "Matrix", "Seurat", "SeuratObject", "SingleCellExperiment", "cowplot", "dplyr", "ggdendro", "ggplot2", "igraph", "reshape2", "scales"] 1379 }, 1380 "ClusterJudge": { 1381 "name": "ClusterJudge", 1382 "version": "1.32.0", 1383 "sha256": "00ybl4r3dhrfi3zagvpn7imd04c6xjd7a9vfyzpd5nk9kkxj5mhz", 1384 "depends": ["httr", "infotheo", "jsonlite", "lattice", "latticeExtra"] 1385 }, 1386 "ClusterSignificance": { 1387 "name": "ClusterSignificance", 1388 "version": "1.38.0", 1389 "sha256": "1h7ik2yryy29sjsr3lgv8g7bqgm0a4b0w3mn10hk0ympaprdjmgd", 1390 "depends": ["RColorBrewer", "pracma", "princurve", "scatterplot3d"] 1391 }, 1392 "CoCiteStats": { 1393 "name": "CoCiteStats", 1394 "version": "1.82.0", 1395 "sha256": "10szmhg289a8i8kcwb55dn4pbaiacgc2lsikn03733rxx81j54pi", 1396 "depends": ["AnnotationDbi", "org_Hs_eg_db"] 1397 }, 1398 "CoGAPS": { 1399 "name": "CoGAPS", 1400 "version": "3.30.0", 1401 "sha256": "1clxww4nmgf1a9swyxz41050nar2svzsqfxj5gy4w29ak0di84p2", 1402 "depends": ["BH", "BiocParallel", "RColorBrewer", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cluster", "dplyr", "fgsea", "forcats", "ggplot2", "gplots", "rhdf5", "testthat"] 1403 }, 1404 "Cogito": { 1405 "name": "Cogito", 1406 "version": "1.16.0", 1407 "sha256": "1bhig4q9pyrsm2gvl2h5j3ll963baqw2lr7d56baa8s5faz9wcw6", 1408 "depends": ["AnnotationDbi", "BiocManager", "GenomicFeatures", "GenomicRanges", "S4Vectors", "Seqinfo", "TxDb_Mmusculus_UCSC_mm9_knownGene", "entropy", "ggplot2", "jsonlite", "magrittr", "rmarkdown"] 1409 }, 1410 "ComPrAn": { 1411 "name": "ComPrAn", 1412 "version": "1.18.0", 1413 "sha256": "1im8vwdllwmrmrdxc2rjjm57896z9rsq3z2gkx27d8yrvvba833p", 1414 "depends": ["DT", "RColorBrewer", "VennDiagram", "data_table", "dplyr", "forcats", "ggplot2", "magrittr", "purrr", "rio", "rlang", "scales", "shiny", "shinydashboard", "shinyjs", "stringr", "tibble", "tidyr"] 1415 }, 1416 "ComplexHeatmap": { 1417 "name": "ComplexHeatmap", 1418 "version": "2.26.0", 1419 "sha256": "1ibphh0x0drr0hm0pk96hs8mgxp5fy6ixs8ak4imyawqdjha3s68", 1420 "depends": ["GetoptLong", "GlobalOptions", "IRanges", "RColorBrewer", "circlize", "clue", "codetools", "colorspace", "digest", "doParallel", "foreach", "matrixStats", "png"] 1421 }, 1422 "CompoundDb": { 1423 "name": "CompoundDb", 1424 "version": "1.14.0", 1425 "sha256": "1zpb8w0ahgfhj28lgzvdaf6540x00gh98lval0i8svgjhb3mk8qj", 1426 "depends": ["AnnotationFilter", "Biobase", "BiocGenerics", "BiocParallel", "ChemmineR", "DBI", "IRanges", "MetaboCoreUtils", "MsCoreUtils", "ProtGenerics", "RSQLite", "S4Vectors", "Spectra", "dbplyr", "dplyr", "jsonlite", "stringi", "tibble", "xml2"] 1427 }, 1428 "ConsensusClusterPlus": { 1429 "name": "ConsensusClusterPlus", 1430 "version": "1.74.0", 1431 "sha256": "1qci7bz3f99lbs1bdjb3sn49751vi1f5367x6cr1246606s72n0f", 1432 "depends": ["ALL", "Biobase", "cluster"] 1433 }, 1434 "CopyNumberPlots": { 1435 "name": "CopyNumberPlots", 1436 "version": "1.26.0", 1437 "sha256": "0vq9jv4lq89x2yp66v075i7wv861z2ph7kzv28nswbivnlwj0763", 1438 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "VariantAnnotation", "cn_mops", "karyoploteR", "regioneR", "rhdf5"] 1439 }, 1440 "Coralysis": { 1441 "name": "Coralysis", 1442 "version": "1.0.0", 1443 "sha256": "15f3jl8na86lbp27al6fhzi7xpyy9hc4gqdcyzm0hjmycfzdzk4x", 1444 "depends": ["BiocParallel", "LiblineaR", "Matrix", "RANN", "RColorBrewer", "RSpectra", "Rtsne", "S4Vectors", "SingleCellExperiment", "SparseM", "SummarizedExperiment", "aricode", "class", "cowplot", "dplyr", "flexclust", "ggplot2", "ggrastr", "ggrepel", "irlba", "matrixStats", "pheatmap", "reshape2", "scatterpie", "scran", "sparseMatrixStats", "tidyr", "umap", "uwot", "withr"] 1445 }, 1446 "CoreGx": { 1447 "name": "CoreGx", 1448 "version": "2.14.0", 1449 "sha256": "189akh4lpbp0dzgflb3nb3vi94bhmsj7qkcl597dnnzxqz00hsb2", 1450 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "BumpyMatrix", "MatrixGenerics", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "bench", "checkmate", "crayon", "data_table", "glue", "lsa", "piano", "rlang"] 1451 }, 1452 "Cormotif": { 1453 "name": "Cormotif", 1454 "version": "1.56.0", 1455 "sha256": "1b8lcm4l6d1zg3laj8gqagfbrc97r2zz0413xcw01h2xxqg5cv46", 1456 "depends": ["affy", "limma"] 1457 }, 1458 "CoverageView": { 1459 "name": "CoverageView", 1460 "version": "1.48.0", 1461 "sha256": "0fnrgacv2ggfzp4i7c9x0368pviw224ldar2nijf5iwi07dhny9a", 1462 "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "rtracklayer"] 1463 }, 1464 "CrispRVariants": { 1465 "name": "CrispRVariants", 1466 "version": "1.38.0", 1467 "sha256": "1msdk4g8qhkqkwi003f33pk0m6mm311ymnggdgzib106iqy1kxb5", 1468 "depends": ["AnnotationDbi", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ggplot2", "gridExtra", "reshape2"] 1469 }, 1470 "CuratedAtlasQueryR": { 1471 "name": "CuratedAtlasQueryR", 1472 "version": "1.8.0", 1473 "sha256": "1hggl8m9hj2mvhkkhs3y44ypra5bsikv4vk97d2qkq6c8q8idrm4", 1474 "depends": ["BiocGenerics", "DBI", "HDF5Array", "S4Vectors", "Seurat", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "assertthat", "cli", "dbplyr", "dplyr", "duckdb", "glue", "httr", "purrr", "rlang", "stringr", "tibble"] 1475 }, 1476 "CyTOFpower": { 1477 "name": "CyTOFpower", 1478 "version": "1.16.0", 1479 "sha256": "1qhli9jf5h62h40zbsxd7q3kgyjxn2afii7s1zv2yb4yz9vpcd55", 1480 "depends": ["CytoGLMM", "DT", "SummarizedExperiment", "diffcyt", "dplyr", "ggplot2", "magrittr", "rlang", "shiny", "shinyFeedback", "shinyMatrix", "shinyjs", "tibble", "tidyr"] 1481 }, 1482 "CytoDx": { 1483 "name": "CytoDx", 1484 "version": "1.30.0", 1485 "sha256": "1jdml013lm0lyyvrgs11q6bi69zlkm8sws4fkg7y3y1i2qnakb7r", 1486 "depends": ["doParallel", "dplyr", "flowCore", "glmnet", "rpart", "rpart_plot"] 1487 }, 1488 "CytoGLMM": { 1489 "name": "CytoGLMM", 1490 "version": "1.18.0", 1491 "sha256": "0kbcb3lzz0mdfwgk5vhbgfj55fx7k6ncq89hrkh4yxx9lsjm2k20", 1492 "depends": ["BiocParallel", "MASS", "Matrix", "RColorBrewer", "caret", "cowplot", "doParallel", "dplyr", "factoextra", "flexmix", "ggplot2", "ggrepel", "logging", "magrittr", "mbest", "pheatmap", "rlang", "stringr", "strucchange", "tibble", "tidyr"] 1493 }, 1494 "CytoMDS": { 1495 "name": "CytoMDS", 1496 "version": "1.6.0", 1497 "sha256": "08iwzasgvgzgc4ihxqwqhj1l56ak4id719v0fgky7r40l4czrqkn", 1498 "depends": ["Biobase", "BiocParallel", "CytoPipeline", "flowCore", "ggforce", "ggplot2", "ggrepel", "patchwork", "pracma", "reshape2", "rlang", "smacof", "transport", "withr"] 1499 }, 1500 "CytoML": { 1501 "name": "CytoML", 1502 "version": "2.22.0", 1503 "sha256": "0my3gpmkqwrh198grwn75mh0wh84p9wpd559s1wgcrzl3ra47y1b", 1504 "depends": ["BH", "Biobase", "RBGL", "RProtoBufLib", "Rgraphviz", "Rhdf5lib", "XML", "cpp11", "cytolib", "data_table", "dplyr", "flowCore", "flowWorkspace", "ggcyto", "graph", "jsonlite", "openCyto", "tibble", "yaml"] 1505 }, 1506 "CytoPipeline": { 1507 "name": "CytoPipeline", 1508 "version": "1.10.0", 1509 "sha256": "1s9341n7az9qs6m7l3m6ks17p46smwhzs861bvnjwr6r9lmi7gpy", 1510 "depends": ["BiocFileCache", "BiocParallel", "PeacoQC", "diagram", "flowAI", "flowCore", "ggcyto", "ggplot2", "jsonlite", "rlang", "scales", "withr"] 1511 }, 1512 "CytoPipelineGUI": { 1513 "name": "CytoPipelineGUI", 1514 "version": "1.8.0", 1515 "sha256": "05x6llzzq4911ydkb0w02j3665bf2414s14nr3r0fs2jb3y7f58w", 1516 "depends": ["CytoPipeline", "flowCore", "ggplot2", "plotly", "shiny"] 1517 }, 1518 "DAMEfinder": { 1519 "name": "DAMEfinder", 1520 "version": "1.22.0", 1521 "sha256": "0gd23z69k0sfds09q0lpz8g3ygj24c1j02ymn8wspq2k7xgivqv6", 1522 "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "bumphunter", "cowplot", "ggplot2", "limma", "plyr", "readr", "reshape2", "stringr"] 1523 }, 1524 "DAPAR": { 1525 "name": "DAPAR", 1526 "version": "1.42.0", 1527 "sha256": "13miss07m8lsnly8nj7mqi9hlwdk9075av9pfi1aahr6bhwx4r43", 1528 "depends": ["Biobase", "DAPARdata", "MSnbase", "foreach", "highcharter"] 1529 }, 1530 "DART": { 1531 "name": "DART", 1532 "version": "1.58.0", 1533 "sha256": "0gswcf08ab1bp0vpx5m66ckd768smvav43h7q4l9plw7sg7pc7mv", 1534 "depends": ["igraph"] 1535 }, 1536 "DCATS": { 1537 "name": "DCATS", 1538 "version": "1.8.0", 1539 "sha256": "00pc0dqf7v1pinbjw62rin9xn24j1bxxy2bf06cj1mwa8ws9fd9k", 1540 "depends": ["MCMCpack", "aod", "e1071", "matrixStats", "robustbase"] 1541 }, 1542 "DECIPHER": { 1543 "name": "DECIPHER", 1544 "version": "3.6.0", 1545 "sha256": "0f344kiriy9q6hnji35fxhvcamb6ac40vwsw250qcj267ldj76wk", 1546 "depends": ["Biostrings", "DBI", "IRanges", "S4Vectors", "XVector"] 1547 }, 1548 "DEFormats": { 1549 "name": "DEFormats", 1550 "version": "1.38.0", 1551 "sha256": "1xjqkv3xwslgm0ifiwcg96hqml7w6v47z8c2q4hf0dk2a9f3sljw", 1552 "depends": ["DESeq2", "GenomicRanges", "S4Vectors", "SummarizedExperiment", "checkmate", "data_table", "edgeR"] 1553 }, 1554 "DEGraph": { 1555 "name": "DEGraph", 1556 "version": "1.62.0", 1557 "sha256": "0ynrw24wx9xhyixv17spkz34bxfx9596arhx4iafjf33pr3b39ys", 1558 "depends": ["KEGGgraph", "NCIgraph", "RBGL", "R_methodsS3", "R_utils", "Rgraphviz", "graph", "lattice", "mvtnorm", "rrcov"] 1559 }, 1560 "DEGreport": { 1561 "name": "DEGreport", 1562 "version": "1.46.0", 1563 "sha256": "0hy8g1v296pjvvgczxkflxhza66fj4x265vljfqsa91zljwcr9lr", 1564 "depends": ["Biobase", "BiocGenerics", "ComplexHeatmap", "ConsensusClusterPlus", "DESeq2", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "broom", "circlize", "cluster", "cowplot", "dendextend", "dplyr", "edgeR", "ggdendro", "ggplot2", "ggrepel", "knitr", "logging", "magrittr", "psych", "reshape", "rlang", "scales", "stringi", "stringr", "tibble", "tidyr"] 1565 }, 1566 "DEGseq": { 1567 "name": "DEGseq", 1568 "version": "1.64.0", 1569 "sha256": "00zsfy9fj89bkr997g9b1si1kvmi346v0xlxnzsassphc2pddfmi", 1570 "depends": ["qvalue"] 1571 }, 1572 "DEP": { 1573 "name": "DEP", 1574 "version": "1.32.0", 1575 "sha256": "1lwj3jz7vkri1kqav7shzxh0y2qdv37f566ss4lm4ifnzihg3y43", 1576 "depends": ["ComplexHeatmap", "DT", "MSnbase", "RColorBrewer", "SummarizedExperiment", "assertthat", "circlize", "cluster", "dplyr", "fdrtool", "ggplot2", "ggrepel", "gridExtra", "imputeLCMD", "limma", "purrr", "readr", "rmarkdown", "shiny", "shinydashboard", "tibble", "tidyr", "vsn"] 1577 }, 1578 "DEScan2": { 1579 "name": "DEScan2", 1580 "version": "1.30.0", 1581 "sha256": "0f2r8008mm1w6gwq6wi8gixwpa1fhcz7h5zarscsbkdyaqmblpqm", 1582 "depends": ["BiocGenerics", "BiocParallel", "ChIPpeakAnno", "DelayedArray", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rcpp", "RcppArmadillo", "S4Vectors", "Seqinfo", "SummarizedExperiment", "data_table", "glue", "plyr", "rtracklayer"] 1583 }, 1584 "DESeq2": { 1585 "name": "DESeq2", 1586 "version": "1.50.0", 1587 "sha256": "18pjr7i0qnfn6h8g1laj6q0ncjmsgqg7jw8icrs35s9dzqy2nglp", 1588 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "MatrixGenerics", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "ggplot2", "locfit", "matrixStats"] 1589 }, 1590 "DESpace": { 1591 "name": "DESpace", 1592 "version": "2.2.0", 1593 "sha256": "1vzkzv18i04734ggdg8wrhbglwcjnn4pywambgz3956rimi8yiib", 1594 "depends": ["BiocGenerics", "BiocParallel", "Matrix", "S4Vectors", "SpatialExperiment", "SummarizedExperiment", "assertthat", "data_table", "dplyr", "edgeR", "ggforce", "ggnewscale", "ggplot2", "limma", "patchwork", "scales", "scuttle", "sf", "spatstat_explore", "spatstat_geom", "terra"] 1595 }, 1596 "DEWSeq": { 1597 "name": "DEWSeq", 1598 "version": "1.24.0", 1599 "sha256": "194w9ky75zmkay98l41sn6129225acf2nlgd8mdvqh1w36l412sh", 1600 "depends": ["BiocGenerics", "BiocParallel", "DESeq2", "GenomicRanges", "R_utils", "S4Vectors", "Seqinfo", "SummarizedExperiment", "data_table"] 1601 }, 1602 "DEXSeq": { 1603 "name": "DEXSeq", 1604 "version": "1.56.0", 1605 "sha256": "1pjy9yxw3w9689bdd5lc3qbxa9820vjdc5dls5jd23c90mmphsyh", 1606 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "DESeq2", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "SummarizedExperiment", "biomaRt", "genefilter", "geneplotter", "hwriter", "statmod", "stringr"] 1607 }, 1608 "DEqMS": { 1609 "name": "DEqMS", 1610 "version": "1.28.0", 1611 "sha256": "0vlglhsgyz8jchfn799navmya7zdr654sad26w0690qlnyzdsqbf", 1612 "depends": ["dplyr", "ggplot2", "limma", "matrixStats"] 1613 }, 1614 "DEsingle": { 1615 "name": "DEsingle", 1616 "version": "1.30.0", 1617 "sha256": "1kg5ak77ip6ncyvf6v1wayf00knxb824xgdlbg56bvjr26ijfnwc", 1618 "depends": ["BiocParallel", "MASS", "Matrix", "VGAM", "bbmle", "gamlss", "maxLik", "pscl"] 1619 }, 1620 "DEsubs": { 1621 "name": "DEsubs", 1622 "version": "1.36.0", 1623 "sha256": "0hmwnx0dpfpw6m2mcgy5ymplj6azfrk21nxmjnabpg7a8i61qj56", 1624 "depends": ["DESeq2", "EBSeq", "Matrix", "NBPSeq", "RBGL", "circlize", "edgeR", "ggplot2", "graph", "igraph", "jsonlite", "limma", "locfit", "pheatmap"] 1625 }, 1626 "DExMA": { 1627 "name": "DExMA", 1628 "version": "1.18.0", 1629 "sha256": "1khhz4mfm1fr1v125hkslhsp85r0x1z2mrni3jrnjasv6nghy2ca", 1630 "depends": ["Biobase", "DExMAdata", "GEOquery", "RColorBrewer", "bnstruct", "impute", "limma", "pheatmap", "plyr", "scales", "snpStats", "sva", "swamp"] 1631 }, 1632 "DFP": { 1633 "name": "DFP", 1634 "version": "1.68.0", 1635 "sha256": "0mhyry6i640hs4b05q99fyh07ark0n2i0xq53432y7v2q61gzahc", 1636 "depends": ["Biobase"] 1637 }, 1638 "DFplyr": { 1639 "name": "DFplyr", 1640 "version": "1.4.0", 1641 "sha256": "1j1wqccxavzslg9mlkb6fdrzrzf6xzdjpwmgbd30y5n0y9gldd07", 1642 "depends": ["BiocGenerics", "S4Vectors", "dplyr", "rlang", "tidyselect"] 1643 }, 1644 "DMCFB": { 1645 "name": "DMCFB", 1646 "version": "1.24.0", 1647 "sha256": "15yr4l1r5y1cf3s28nxpmdzak0akks2z4phmcn5dmmy5j7fzv9zz", 1648 "depends": ["BiocParallel", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "SummarizedExperiment", "arm", "benchmarkme", "data_table", "fastDummies", "matrixStats", "rtracklayer", "speedglm", "tibble"] 1649 }, 1650 "DMCHMM": { 1651 "name": "DMCHMM", 1652 "version": "1.32.0", 1653 "sha256": "0s8nng5gqal4c7nn3m7z5kzggwgsji6jnzmr0mh233zpqz31kj2h", 1654 "depends": ["BiocParallel", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "calibrate", "fdrtool", "multcomp", "rtracklayer"] 1655 }, 1656 "DMRScan": { 1657 "name": "DMRScan", 1658 "version": "1.32.0", 1659 "sha256": "0f4wmw9j7iwhwhbrdc8pbv5cb72yhz7w838k0xhv65sa92d9h93g", 1660 "depends": ["GenomicRanges", "IRanges", "MASS", "Matrix", "RcppRoll", "Seqinfo", "mvtnorm"] 1661 }, 1662 "DMRcaller": { 1663 "name": "DMRcaller", 1664 "version": "1.42.0", 1665 "sha256": "0v1jylpj5phgjszy67b4q4d5ac31k4v3np27nvvlbckh7ga5bz0m", 1666 "depends": ["BSgenome", "BiocManager", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "InteractionSet", "Rcpp", "RcppRoll", "Rsamtools", "S4Vectors", "Seqinfo", "betareg", "inflection", "stringr"] 1667 }, 1668 "DMRcate": { 1669 "name": "DMRcate", 1670 "version": "3.6.0", 1671 "sha256": "04hvb65i267365qgjmqbd2lbk5fxnn4r5vd37ncvbq0gn71qax7c", 1672 "depends": ["AnnotationHub", "ExperimentHub", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "Seqinfo", "SummarizedExperiment", "biomaRt", "bsseq", "edgeR", "limma", "minfi", "missMethyl", "plyr"] 1673 }, 1674 "DNABarcodeCompatibility": { 1675 "name": "DNABarcodeCompatibility", 1676 "version": "1.26.0", 1677 "sha256": "0mjbnq9aka47qi212y4dk7vrwq9jldl68k3x06jdsl5j1xid120c", 1678 "depends": ["BH", "Rcpp", "dplyr", "numbers", "purrr", "stringr", "tidyr"] 1679 }, 1680 "DNABarcodes": { 1681 "name": "DNABarcodes", 1682 "version": "1.40.0", 1683 "sha256": "0cvgbpimjl4wswq95d4zrxvfq9z6fl11lg70727l78xhd9vh3i4d", 1684 "depends": ["BH", "Matrix", "Rcpp"] 1685 }, 1686 "DNAcopy": { 1687 "name": "DNAcopy", 1688 "version": "1.84.0", 1689 "sha256": "1z08nz7qawhh2rrq4sc725vm1pi86j6c4rw9fjpbivdh7wl36a6p", 1690 "depends": [] 1691 }, 1692 "DNAcycP2": { 1693 "name": "DNAcycP2", 1694 "version": "1.2.0", 1695 "sha256": "1cn4ifnc03qjfzw37ycn95bm2sc2pksyryl0v783yhvpbplfzbih", 1696 "depends": ["basilisk", "reticulate"] 1697 }, 1698 "DNAfusion": { 1699 "name": "DNAfusion", 1700 "version": "1.12.0", 1701 "sha256": "14hf9fjr0fn8r5k853wc0fcfy6xjrpiz6269l058q9fqanwwml90", 1702 "depends": ["BiocBaseUtils", "BiocGenerics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "TxDb_Hsapiens_UCSC_hg38_knownGene"] 1703 }, 1704 "DNAshapeR": { 1705 "name": "DNAshapeR", 1706 "version": "1.38.0", 1707 "sha256": "0069dcaa6dyjqclmdcmfwp16nl7mbxcdvl6kqii6xx5q6ha4khyj", 1708 "depends": ["Biostrings", "GenomicRanges", "Rcpp", "fields"] 1709 }, 1710 "DNEA": { 1711 "name": "DNEA", 1712 "version": "1.0.0", 1713 "sha256": "0fb16yraaxnp2ap4wk68vkr9ac3cgy37xjmkrsmwrjxiwfrmvmjm", 1714 "depends": ["BiocParallel", "Matrix", "SummarizedExperiment", "dplyr", "gdata", "glasso", "igraph", "janitor", "netgsa", "stringr"] 1715 }, 1716 "DOSE": { 1717 "name": "DOSE", 1718 "version": "4.4.0", 1719 "sha256": "0d6lwlkinjf66snfxg3j85m12vw00nmc507px871bi9p4xq7zjld", 1720 "depends": ["AnnotationDbi", "BiocParallel", "GOSemSim", "fgsea", "ggplot2", "qvalue", "reshape2", "yulab_utils"] 1721 }, 1722 "DOtools": { 1723 "name": "DOtools", 1724 "version": "1.0.0", 1725 "sha256": "1g78ljyr71x1v9srnz9m7v4gkc1dbyqgsbkaqfpdmvs5ybwxrkg3", 1726 "depends": ["DESeq2", "DropletUtils", "Matrix", "S4Vectors", "SCpubr", "Seurat", "SeuratObject", "SingleCellExperiment", "basilisk", "cli", "cowplot", "curl", "dplyr", "enrichR", "ggalluvial", "ggcorrplot", "ggiraphExtra", "ggplot2", "ggpubr", "ggtext", "magrittr", "openxlsx", "progress", "purrr", "reshape2", "reticulate", "rlang", "rstatix", "scCustomize", "scDblFinder", "scales", "tibble", "tidyr", "tidyverse", "zellkonverter"] 1727 }, 1728 "DRIMSeq": { 1729 "name": "DRIMSeq", 1730 "version": "1.38.0", 1731 "sha256": "0ga00qvrlccawq9nl0vdpsd9gbqx1xcafdxflp7vpi85s04bmg48", 1732 "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "edgeR", "ggplot2", "limma", "reshape2"] 1733 }, 1734 "DSS": { 1735 "name": "DSS", 1736 "version": "2.58.0", 1737 "sha256": "0k9vw11xxdi1d2qjp7z9kwzhcqb2d80wi76xvmqnmrl810ni07a5", 1738 "depends": ["Biobase", "BiocParallel", "bsseq"] 1739 }, 1740 "DTA": { 1741 "name": "DTA", 1742 "version": "2.56.0", 1743 "sha256": "0xvwa03kivly6617l4lbwz78xzhz5qn7f05pn9a1qxgg2fxxw2mf", 1744 "depends": ["LSD", "scatterplot3d"] 1745 }, 1746 "DaMiRseq": { 1747 "name": "DaMiRseq", 1748 "version": "2.22.0", 1749 "sha256": "1gm0wd304gd6xp339z6977yx0iwn3zqqf249hw882yi059xj295s", 1750 "depends": ["DESeq2", "EDASeq", "FSelector", "FactoMineR", "Hmisc", "MASS", "RColorBrewer", "RSNNS", "SummarizedExperiment", "arm", "caret", "corrplot", "e1071", "edgeR", "ggplot2", "ineq", "kknn", "limma", "lubridate", "pheatmap", "pls", "plsVarSel", "plyr", "randomForest", "reshape2", "sva"] 1751 }, 1752 "Damsel": { 1753 "name": "Damsel", 1754 "version": "1.6.0", 1755 "sha256": "08d2kpqrvs00l6j4dpibflzy55wpsfdqrxpnbb84dk6x85j0cr0r", 1756 "depends": ["AnnotationDbi", "Biostrings", "ComplexHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Rsamtools", "Rsubread", "dplyr", "edgeR", "ggbio", "ggplot2", "goseq", "magrittr", "patchwork", "plyranges", "reshape2", "rlang", "stringr", "tidyr"] 1757 }, 1758 "DeMAND": { 1759 "name": "DeMAND", 1760 "version": "1.40.0", 1761 "sha256": "08pkxdhxzw2d4fx1r6h8b10bwkhhaipdr5fy6c5vh89z1lbjmxcg", 1762 "depends": ["KernSmooth"] 1763 }, 1764 "DeMixT": { 1765 "name": "DeMixT", 1766 "version": "1.26.0", 1767 "sha256": "0nqalk74r8k1sr1wc3n60dp19crv8arp3xczv371c29wvhgfmqn8", 1768 "depends": ["DSS", "KernSmooth", "Rcpp", "SummarizedExperiment", "base64enc", "dendextend", "ggplot2", "knitr", "matrixStats", "matrixcalc", "psych", "rmarkdown", "sva", "truncdist"] 1769 }, 1770 "DeconvoBuddies": { 1771 "name": "DeconvoBuddies", 1772 "version": "1.2.0", 1773 "sha256": "1q6zcp83yqnlifasz8dp37f9a6fh97fxlfjydm67gsqc7vcsiv7d", 1774 "depends": ["AnnotationHub", "BiocFileCache", "DelayedMatrixStats", "ExperimentHub", "MatrixGenerics", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "purrr", "rafalib", "reshape2", "scran", "spatialLIBD", "stringr", "tibble"] 1775 }, 1776 "DeeDeeExperiment": { 1777 "name": "DeeDeeExperiment", 1778 "version": "1.0.0", 1779 "sha256": "05sycr3kv44w3x66s280vp1nz4i8pxflxqrw1lwffg087ssbyp23", 1780 "depends": ["DESeq2", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cli", "edgeR", "limma"] 1781 }, 1782 "DeepPINCS": { 1783 "name": "DeepPINCS", 1784 "version": "1.18.0", 1785 "sha256": "0p9hiqhv2kr44jw61bsg15ymxqzdxkq5vvywsgw2418428d3j2gp", 1786 "depends": ["CatEncoders", "PRROC", "keras", "matlab", "purrr", "rcdk", "reticulate", "stringdist", "tensorflow", "tokenizers", "ttgsea", "webchem"] 1787 }, 1788 "DeepTarget": { 1789 "name": "DeepTarget", 1790 "version": "1.4.0", 1791 "sha256": "1fyr7y6bv4bgx6hsjac0zjh8h7i14qvxf6vhwnaj0kc5nprszzbn", 1792 "depends": ["BiocParallel", "depmap", "dplyr", "fgsea", "ggplot2", "ggpubr", "pROC", "readr", "stringr"] 1793 }, 1794 "DegCre": { 1795 "name": "DegCre", 1796 "version": "1.6.0", 1797 "sha256": "056716y8ychdbac6mvyp99n3ak5afnxgyksa1b524jzwipc3w0k9", 1798 "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "Seqinfo", "TxDb_Hsapiens_UCSC_hg38_knownGene", "org_Hs_eg_db", "plotgardener", "qvalue"] 1799 }, 1800 "DegNorm": { 1801 "name": "DegNorm", 1802 "version": "1.20.0", 1803 "sha256": "1737fdfd5i80qh4dp21z5pq4d3xfzl79m59qwhmz40pljx98bl88", 1804 "depends": ["GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rcpp", "RcppArmadillo", "Rsamtools", "S4Vectors", "data_table", "doParallel", "foreach", "ggplot2", "heatmaply", "plotly", "plyr", "txdbmaker", "viridis"] 1805 }, 1806 "DelayedArray": { 1807 "name": "DelayedArray", 1808 "version": "0.36.0", 1809 "sha256": "1x5qhgnwf89hmra4lvs0sa5mqz9rm45bmw4q1469zw1brazcp3gv", 1810 "depends": ["BiocGenerics", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors", "SparseArray"] 1811 }, 1812 "DelayedDataFrame": { 1813 "name": "DelayedDataFrame", 1814 "version": "1.26.0", 1815 "sha256": "1yqvpkps2kcfdaadnh52rmhqa0z37579i9f1ff86xablmzi9znfg", 1816 "depends": ["BiocGenerics", "DelayedArray", "S4Vectors"] 1817 }, 1818 "DelayedMatrixStats": { 1819 "name": "DelayedMatrixStats", 1820 "version": "1.32.0", 1821 "sha256": "0ygp9p8lm19421ybqsrp0xz396cpf7b2vwk6hmrr5gxhxqqxyba5", 1822 "depends": ["DelayedArray", "IRanges", "Matrix", "MatrixGenerics", "S4Vectors", "SparseArray", "sparseMatrixStats"] 1823 }, 1824 "DelayedRandomArray": { 1825 "name": "DelayedRandomArray", 1826 "version": "1.18.0", 1827 "sha256": "039m4n7vd56vgnf1nxfga3f7f4sd533qy3wjb77ly9pfs2jnb546", 1828 "depends": ["BH", "DelayedArray", "Rcpp", "SparseArray", "dqrng"] 1829 }, 1830 "DelayedTensor": { 1831 "name": "DelayedTensor", 1832 "version": "1.16.0", 1833 "sha256": "1wzjdmqmrgakkzsdjj7qpd9r6i07skq3l7hxkj3qlrfxp91rgad2", 1834 "depends": ["BiocSingular", "DelayedArray", "DelayedRandomArray", "HDF5Array", "Matrix", "S4Arrays", "SparseArray", "einsum", "irlba", "rTensor"] 1835 }, 1836 "DepInfeR": { 1837 "name": "DepInfeR", 1838 "version": "1.14.0", 1839 "sha256": "0pgxxlsa72h57592yrhz5n4i2332mphrjd32019vhiisligcadzr", 1840 "depends": ["BiocParallel", "glmnet", "matrixStats"] 1841 }, 1842 "DepecheR": { 1843 "name": "DepecheR", 1844 "version": "1.26.0", 1845 "sha256": "063jx19fs7gx84ivsmfs47lw5i79037v4c31k50jfzbxnwb1bnnc", 1846 "depends": ["ClusterR", "FNN", "MASS", "Rcpp", "RcppEigen", "beanplot", "collapse", "doSNOW", "dplyr", "foreach", "ggplot2", "gmodels", "gplots", "matrixStats", "mixOmics", "moments", "reshape2", "robustbase", "viridis"] 1847 }, 1848 "DiffBind": { 1849 "name": "DiffBind", 1850 "version": "3.20.0", 1851 "sha256": "1y2i85mcs4wgkl10ykmfhvikapb3kql7v4jwli99jlvi897xwjsq", 1852 "depends": ["BiocParallel", "DESeq2", "GenomicAlignments", "GenomicRanges", "GreyListChIP", "IRanges", "RColorBrewer", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "SummarizedExperiment", "amap", "apeglm", "ashr", "dplyr", "ggplot2", "ggrepel", "gplots", "lattice", "limma", "locfit", "systemPipeR"] 1853 }, 1854 "DiffLogo": { 1855 "name": "DiffLogo", 1856 "version": "2.34.0", 1857 "sha256": "08wgvbjqwkrqdmh6xiyr1slvq4yasl70g6r8xlw11j1ipqrr37g4", 1858 "depends": ["cba"] 1859 }, 1860 "DifferentialRegulation": { 1861 "name": "DifferentialRegulation", 1862 "version": "2.8.0", 1863 "sha256": "09vbnd9as1925m9h2dhxxg8zwrqnjpql1qvkdx7c7rqm9wfhm6bx", 1864 "depends": ["BANDITS", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "SingleCellExperiment", "SummarizedExperiment", "data_table", "doParallel", "doRNG", "foreach", "ggplot2", "gridExtra", "tximport"] 1865 }, 1866 "Dino": { 1867 "name": "Dino", 1868 "version": "1.16.0", 1869 "sha256": "1miqqyf792ijrc2b7rbwgl7yfbyng68wylip88230yik8jmdhdvp", 1870 "depends": ["BiocParallel", "BiocSingular", "Matrix", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "matrixStats", "scran"] 1871 }, 1872 "DirichletMultinomial": { 1873 "name": "DirichletMultinomial", 1874 "version": "1.52.0", 1875 "sha256": "0mr7b6xvi841k2whmp1qwh6nys7fkd2d5m0zzsp5m76lq24hhjdn", 1876 "depends": ["BiocGenerics", "IRanges", "S4Vectors"] 1877 }, 1878 "DiscoRhythm": { 1879 "name": "DiscoRhythm", 1880 "version": "1.26.0", 1881 "sha256": "0dgsfnw1zvf7m3z20wdakpv64yilq47lyj8cklkqs4kg2ks38cjc", 1882 "depends": ["BiocGenerics", "BiocStyle", "DT", "MetaCycle", "S4Vectors", "SummarizedExperiment", "UpSetR", "VennDiagram", "broom", "data_table", "dplyr", "ggExtra", "ggplot2", "gridExtra", "heatmaply", "kableExtra", "knitr", "magick", "matrixStats", "matrixTests", "plotly", "reshape2", "rmarkdown", "shiny", "shinyBS", "shinycssloaders", "shinydashboard", "shinyjs", "viridis", "zip"] 1883 }, 1884 "DominoEffect": { 1885 "name": "DominoEffect", 1886 "version": "1.30.0", 1887 "sha256": "1i59118bqk25jqkjkg6ddc8xyls9dd2r15piw7a6rgf8d2hv395s", 1888 "depends": ["AnnotationDbi", "Biostrings", "GenomicRanges", "IRanges", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "biomaRt", "data_table", "pwalign"] 1889 }, 1890 "Doscheda": { 1891 "name": "Doscheda", 1892 "version": "1.32.0", 1893 "sha256": "0dllqkqh9760hl9qjwqdz6npsprp48zw5rb4didj7ff13yl4nzbn", 1894 "depends": ["DT", "affy", "calibrate", "corrgram", "drc", "ggplot2", "gridExtra", "httr", "jsonlite", "limma", "matrixStats", "prodlim", "readxl", "reshape2", "shiny", "shinydashboard", "stringr", "vsn"] 1895 }, 1896 "DriverNet": { 1897 "name": "DriverNet", 1898 "version": "1.50.0", 1899 "sha256": "1sy3jzbg2hh83s1w6qm9mi4qk3ppa5xzc8h59ylm0pr42mnhmfwg", 1900 "depends": [] 1901 }, 1902 "DropletUtils": { 1903 "name": "DropletUtils", 1904 "version": "1.30.0", 1905 "sha256": "18k2jlz9yk2fayk01q165cp0wr1sb3hq73q6fp0w3w669ykfz0a5", 1906 "depends": ["BH", "BiocGenerics", "BiocParallel", "DelayedArray", "DelayedMatrixStats", "GenomicRanges", "HDF5Array", "IRanges", "Matrix", "R_utils", "Rcpp", "Rhdf5lib", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "assorthead", "beachmat", "dqrng", "edgeR", "rhdf5", "scuttle"] 1907 }, 1908 "DrugVsDisease": { 1909 "name": "DrugVsDisease", 1910 "version": "2.52.0", 1911 "sha256": "1dgj492s26sbmxs8ac36cv6w9g6d4ay7p56hy3d5smmk21r5fsj7", 1912 "depends": ["ArrayExpress", "BiocGenerics", "DrugVsDiseasedata", "GEOquery", "RUnit", "affy", "annotate", "biomaRt", "cMap2data", "hgu133a2_db", "hgu133a_db", "hgu133plus2_db", "limma", "qvalue", "xtable"] 1913 }, 1914 "DspikeIn": { 1915 "name": "DspikeIn", 1916 "version": "1.0.0", 1917 "sha256": "0rdvkj2ncsvzj5zm2msq02aakx4g9yzsc63v873jk15y2ywncmsm", 1918 "depends": ["Biostrings", "DECIPHER", "DESeq2", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "data_table", "dplyr", "edgeR", "flextable", "ggalluvial", "ggnewscale", "ggplot2", "ggpubr", "ggraph", "ggrepel", "ggridges", "ggstar", "ggtree", "ggtreeExtra", "igraph", "limma", "matrixStats", "microbiome", "msa", "officer", "patchwork", "phangorn", "phyloseq", "randomForest", "reshape2", "rlang", "scales", "tibble", "tidyr", "xml2"] 1919 }, 1920 "Dune": { 1921 "name": "Dune", 1922 "version": "1.22.0", 1923 "sha256": "17vqzbl0zvmg1ndv99812hqmr6m8s14mw8bsa0mlv2piqh3iz5hs", 1924 "depends": ["BiocParallel", "RColorBrewer", "SummarizedExperiment", "aricode", "dplyr", "gganimate", "ggplot2", "magrittr", "purrr", "tidyr"] 1925 }, 1926 "DuplexDiscovereR": { 1927 "name": "DuplexDiscovereR", 1928 "version": "1.4.0", 1929 "sha256": "101ppsi4inl7c7np8aqchdr4kabqxpyvmr5g14akmyp5hdqy7jgc", 1930 "depends": ["Biostrings", "GenomicAlignments", "GenomicRanges", "Gviz", "InteractionSet", "dplyr", "ggsci", "igraph", "purrr", "rlang", "rtracklayer", "scales", "stringr", "tibble", "tidyr", "vctrs"] 1931 }, 1932 "DynDoc": { 1933 "name": "DynDoc", 1934 "version": "1.88.0", 1935 "sha256": "09nf883xlqwjisyab3vryvrv33z7zllpqi1zppyndxygm524avbp", 1936 "depends": [] 1937 }, 1938 "EBImage": { 1939 "name": "EBImage", 1940 "version": "4.52.0", 1941 "sha256": "171c233hqpssqsf2j0ifmabnxg5q0ysdvz8s7wrld0xbxls1fyj2", 1942 "depends": ["BiocGenerics", "RCurl", "abind", "fftwtools", "htmltools", "htmlwidgets", "jpeg", "locfit", "png", "tiff"] 1943 }, 1944 "EBSEA": { 1945 "name": "EBSEA", 1946 "version": "1.38.0", 1947 "sha256": "1qcflilq5abcymhdpzypdqs5y6r0wa4wbv4g17m4z22f0vag6qy9", 1948 "depends": ["DESeq2", "EmpiricalBrownsMethod"] 1949 }, 1950 "EBSeq": { 1951 "name": "EBSeq", 1952 "version": "2.8.0", 1953 "sha256": "1d9hvmh7dx8alf11xh3pc7il0jfr5jsbqjn90rrarsmslbkys7la", 1954 "depends": ["BH", "Rcpp", "RcppEigen", "blockmodeling", "gplots", "testthat"] 1955 }, 1956 "EBarrays": { 1957 "name": "EBarrays", 1958 "version": "2.74.0", 1959 "sha256": "12x2c3qvybiick7pk5cl9i3ndg1vgwkv08i6dgd8gqf83dvwylk1", 1960 "depends": ["Biobase", "cluster", "lattice"] 1961 }, 1962 "EBcoexpress": { 1963 "name": "EBcoexpress", 1964 "version": "1.54.0", 1965 "sha256": "08smy75js91pfwl8vb6s97g8j7i7g5j8ycidfxcgdnf1i5nylkmh", 1966 "depends": ["EBarrays", "mclust", "minqa"] 1967 }, 1968 "EDASeq": { 1969 "name": "EDASeq", 1970 "version": "2.44.0", 1971 "sha256": "1j8q66dba91pdc39khnfq4fdwky9w5lrvps5adl7xcqv73ryw59p", 1972 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocManager", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "ShortRead", "aroma_light", "biomaRt"] 1973 }, 1974 "EDIRquery": { 1975 "name": "EDIRquery", 1976 "version": "1.10.0", 1977 "sha256": "1lj0h2hzfmil3zvsn1dr7k70pc4jlzvnn5k0f8pf6n9g1am2rrbn", 1978 "depends": ["GenomicRanges", "InteractionSet", "readr", "tibble", "tictoc"] 1979 }, 1980 "EGAD": { 1981 "name": "EGAD", 1982 "version": "1.38.0", 1983 "sha256": "13xw27sjc4v0gc9ln7qfa8swwd3jqr0032nknfh1yr3zk8sz4sy8", 1984 "depends": ["Biobase", "GEOquery", "MASS", "RColorBrewer", "RCurl", "gplots", "igraph", "impute", "limma", "plyr", "zoo"] 1985 }, 1986 "EGSEA": { 1987 "name": "EGSEA", 1988 "version": "1.38.0", 1989 "sha256": "1kmhld8fnd6cwxd0k7i9mzh8hq22s2n6n4gqg8nwpvgvw2i2h2v3", 1990 "depends": ["AnnotationDbi", "Biobase", "DT", "EGSEAdata", "GSVA", "HTMLUtils", "PADOG", "RColorBrewer", "edgeR", "gage", "ggplot2", "globaltest", "gplots", "htmlwidgets", "hwriter", "limma", "metap", "org_Hs_eg_db", "org_Mm_eg_db", "org_Rn_eg_db", "pathview", "plotly", "safe", "stringi", "topGO"] 1991 }, 1992 "ELMER": { 1993 "name": "ELMER", 1994 "version": "2.33.1", 1995 "sha256": "1ajwq8amzif2sxyz11a8axbd4jibp3f7pzrcl9f9zbwz8l5h6jmx", 1996 "depends": ["ComplexHeatmap", "DelayedArray", "ELMER_data", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Matrix", "MultiAssayExperiment", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TCGAbiolinks", "biomaRt", "circlize", "doParallel", "downloader", "dplyr", "ggplot2", "ggpubr", "ggrepel", "gridExtra", "lattice", "magrittr", "plotly", "plyr", "progress", "purrr", "readr", "reshape", "reshape2", "rmarkdown", "rtracklayer", "rvest", "scales", "stringr", "tibble", "tidyr", "xml2"] 1997 }, 1998 "ELViS": { 1999 "name": "ELViS", 2000 "version": "1.2.0", 2001 "sha256": "0fj5x8iz4qp29rffh14cz71dn0kzw2rhvdxgr6l92ixa29l2bsnz", 2002 "depends": ["BiocGenerics", "ComplexHeatmap", "GenomicFeatures", "GenomicRanges", "IRanges", "circlize", "data_table", "dplyr", "ggplot2", "glue", "igraph", "magrittr", "memoise", "patchwork", "reticulate", "scales", "segclust2d", "stringr", "txdbmaker", "uuid", "zoo"] 2003 }, 2004 "EMDomics": { 2005 "name": "EMDomics", 2006 "version": "2.40.0", 2007 "sha256": "16zfssk8f2id1vaklgvrk986jr0zzqzxacm439x29lnn2fkh4fkr", 2008 "depends": ["BiocParallel", "CDFt", "emdist", "ggplot2", "matrixStats", "preprocessCore"] 2009 }, 2010 "ENmix": { 2011 "name": "ENmix", 2012 "version": "1.46.0", 2013 "sha256": "1zv7b8yfzn3mazfg2hyc20xpi8ayd0xwxz5wnd4ywjmnfagwqjwb", 2014 "depends": ["AnnotationHub", "Biobase", "ExperimentHub", "IRanges", "RPMM", "S4Vectors", "SummarizedExperiment", "doParallel", "dynamicTreeCut", "foreach", "genefilter", "geneplotter", "gplots", "gtools", "illuminaio", "impute", "irlba", "matrixStats", "minfi", "quadprog"] 2015 }, 2016 "ERSSA": { 2017 "name": "ERSSA", 2018 "version": "1.28.0", 2019 "sha256": "1bj2djhvawy5kg059syg3sbwdjl092kf5vaxjh1zg204nn760fx0", 2020 "depends": ["BiocParallel", "DESeq2", "RColorBrewer", "apeglm", "edgeR", "ggplot2", "plyr"] 2021 }, 2022 "EWCE": { 2023 "name": "EWCE", 2024 "version": "1.18.0", 2025 "sha256": "0i476appzbnv6gy8jhpwnfaq6dqhfpny56m7w2l7a2j6qgyifmva", 2026 "depends": ["BiocParallel", "DelayedArray", "HGNChelper", "Matrix", "RNOmni", "SingleCellExperiment", "SummarizedExperiment", "data_table", "dplyr", "ewceData", "ggplot2", "limma", "orthogene", "reshape2", "stringr"] 2027 }, 2028 "EasyCellType": { 2029 "name": "EasyCellType", 2030 "version": "1.12.0", 2031 "sha256": "0c4x827v95dz9h3b632f3si3nz5fjqawzzhfkh9ralfhqfzpm9kq", 2032 "depends": ["AnnotationDbi", "BiocStyle", "clusterProfiler", "dplyr", "forcats", "ggplot2", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "rlang", "vctrs"] 2033 }, 2034 "EmpiricalBrownsMethod": { 2035 "name": "EmpiricalBrownsMethod", 2036 "version": "1.38.0", 2037 "sha256": "0ff4sqgg3j8m74li69p7b9rkckwfgkr2igy5k3iz485qq2g8iryg", 2038 "depends": [] 2039 }, 2040 "EnMCB": { 2041 "name": "EnMCB", 2042 "version": "1.22.0", 2043 "sha256": "1fnz58vc1j7zacwj12f045sachfbdy6apkd8b036gnqrdkf49c88", 2044 "depends": ["BiocFileCache", "Matrix", "boot", "e1071", "ggplot2", "glmnet", "igraph", "mboost", "rms", "survival", "survivalROC", "survivalsvm"] 2045 }, 2046 "EnrichDO": { 2047 "name": "EnrichDO", 2048 "version": "1.4.0", 2049 "sha256": "1h36v3m4all9n05s9mwcidlz27rxawibdl1kanyf2s89a3h0jj9d", 2050 "depends": ["BiocGenerics", "Rgraphviz", "S4Vectors", "dplyr", "ggplot2", "graph", "hash", "magrittr", "pheatmap", "purrr", "tidyr"] 2051 }, 2052 "EnrichedHeatmap": { 2053 "name": "EnrichedHeatmap", 2054 "version": "1.40.0", 2055 "sha256": "1pz5czpy4dhjxaamz7n7zvxz3s48jyk3rhy90pqil41i8zlql4hr", 2056 "depends": ["ComplexHeatmap", "GenomicRanges", "GetoptLong", "IRanges", "Rcpp", "circlize", "locfit", "matrixStats"] 2057 }, 2058 "EnrichmentBrowser": { 2059 "name": "EnrichmentBrowser", 2060 "version": "2.40.0", 2061 "sha256": "0qvp3j5fxxy97v29qj8ywgq0s2x1s7n222rmhq2lyb8vxyc7i0rd", 2062 "depends": ["AnnotationDbi", "BiocFileCache", "BiocManager", "GO_db", "GSEABase", "KEGGREST", "KEGGgraph", "Rgraphviz", "S4Vectors", "SPIA", "SummarizedExperiment", "edgeR", "graph", "graphite", "hwriter", "limma", "pathview", "safe"] 2063 }, 2064 "EpiCompare": { 2065 "name": "EpiCompare", 2066 "version": "1.14.0", 2067 "sha256": "1ca9vzlwpyiqv3y3f9j6ch0wv2545wiza54dp2iyn8cfhph8s67q", 2068 "depends": ["AnnotationHub", "BiocGenerics", "ChIPseeker", "GenomeInfoDb", "GenomicRanges", "IRanges", "Seqinfo", "data_table", "downloadthis", "genomation", "ggplot2", "htmltools", "plotly", "reshape2", "rmarkdown", "rtracklayer", "stringr"] 2069 }, 2070 "EpiDISH": { 2071 "name": "EpiDISH", 2072 "version": "2.26.0", 2073 "sha256": "15p5qshjbas5fb3x2sdwpcxd9ps91y4089jjy8c12q7sail4c54q", 2074 "depends": ["MASS", "Matrix", "e1071", "locfdr", "matrixStats", "quadprog", "stringr"] 2075 }, 2076 "EpiMix": { 2077 "name": "EpiMix", 2078 "version": "1.12.0", 2079 "sha256": "1swwxf3hq3wcn05q1yxy5djby7jn35plylwnli27rrfqqrvi05h5", 2080 "depends": ["AnnotationDbi", "AnnotationHub", "Biobase", "ELMER_data", "EpiMix_data", "ExperimentHub", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "RCurl", "RPMM", "R_matlab", "S4Vectors", "Seqinfo", "SummarizedExperiment", "biomaRt", "data_table", "doParallel", "doSNOW", "downloader", "dplyr", "foreach", "ggplot2", "impute", "limma", "plyr", "progress", "rlang", "tibble", "tidyr"] 2081 }, 2082 "EpiTxDb": { 2083 "name": "EpiTxDb", 2084 "version": "1.22.0", 2085 "sha256": "185m3wvqji8qw3bc05cmpzki1df5i8kr7hw15dnpnpich9i0mi3r", 2086 "depends": ["AnnotationDbi", "BiocFileCache", "BiocGenerics", "Biostrings", "DBI", "GenomicFeatures", "GenomicRanges", "IRanges", "Modstrings", "RSQLite", "S4Vectors", "Seqinfo", "curl", "httr", "rex", "tRNAdbImport", "txdbmaker", "xml2"] 2087 }, 2088 "EpipwR": { 2089 "name": "EpipwR", 2090 "version": "1.4.0", 2091 "sha256": "11rwbvskmx75cwbmq7c5s10vjwhgj2ibwy8g0zqvwlmsa2dynd4w", 2092 "depends": ["EpipwR_data", "ExperimentHub", "ggplot2"] 2093 }, 2094 "EventPointer": { 2095 "name": "EventPointer", 2096 "version": "3.18.0", 2097 "sha256": "0zf4dc8pa5b93il4qpnbc6g9c7ir0rqhxa8w1vhghdwqswjb74ig", 2098 "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "Matrix", "RBGL", "S4Vectors", "SGSeq", "SummarizedExperiment", "abind", "affxparser", "cobs", "doParallel", "fgsea", "foreach", "glmnet", "graph", "igraph", "iterators", "limma", "lpSolve", "matrixStats", "nnls", "poibin", "prodlim", "qvalue", "rhdf5", "speedglm", "stringr", "tximport"] 2099 }, 2100 "ExCluster": { 2101 "name": "ExCluster", 2102 "version": "1.28.0", 2103 "sha256": "1103xdpcv59nsb2wk5qg9dmw6x6nfp18b9d3c3dsmb5bbl4hyy57", 2104 "depends": ["GenomicRanges", "IRanges", "Rsubread", "matrixStats", "rtracklayer"] 2105 }, 2106 "ExiMiR": { 2107 "name": "ExiMiR", 2108 "version": "2.52.0", 2109 "sha256": "12075cp6py3ns59gyj2snrp6yr7v0zxwnvmnzfprynixhiiqzw2z", 2110 "depends": ["Biobase", "affy", "affyio", "limma", "preprocessCore"] 2111 }, 2112 "ExperimentHub": { 2113 "name": "ExperimentHub", 2114 "version": "3.0.0", 2115 "sha256": "1ghz228x3ijr003zldqh9b473wn8cc518w6iwzx03sgrxaq2s177", 2116 "depends": ["AnnotationHub", "BiocFileCache", "BiocGenerics", "BiocManager", "S4Vectors", "rappdirs"] 2117 }, 2118 "ExperimentHubData": { 2119 "name": "ExperimentHubData", 2120 "version": "1.36.0", 2121 "sha256": "1bjqvlhmzznsvji8k5d24wqhkpr8bhafjhmsqbnd8m58k3nrx919", 2122 "depends": ["AnnotationHubData", "BiocGenerics", "BiocManager", "DBI", "ExperimentHub", "S4Vectors", "curl", "httr"] 2123 }, 2124 "ExperimentSubset": { 2125 "name": "ExperimentSubset", 2126 "version": "1.20.0", 2127 "sha256": "1yw4ci223s5cc0kwz6frfp3wngws48bghxwx6r761n03wsxs4g2q", 2128 "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "TreeSummarizedExperiment"] 2129 }, 2130 "ExploreModelMatrix": { 2131 "name": "ExploreModelMatrix", 2132 "version": "1.22.0", 2133 "sha256": "0mbgsq3kb5wz9dz75hq4bka69in08kcyii8hqpga09948ffgm03l", 2134 "depends": ["DT", "MASS", "S4Vectors", "cowplot", "dplyr", "ggplot2", "limma", "magrittr", "rintrojs", "rlang", "scales", "shiny", "shinydashboard", "shinyjs", "tibble", "tidyr"] 2135 }, 2136 "ExpressionAtlas": { 2137 "name": "ExpressionAtlas", 2138 "version": "2.2.0", 2139 "sha256": "0zksi7r2r98kid5w785spshnw8pgw8za3snag9k5qmycryhwvwfr", 2140 "depends": ["Biobase", "BiocStyle", "RCurl", "S4Vectors", "SummarizedExperiment", "XML", "httr", "jsonlite", "limma", "xml2"] 2141 }, 2142 "FEAST": { 2143 "name": "FEAST", 2144 "version": "1.18.0", 2145 "sha256": "0yraanabz295kj3xlcllfscb7lvjk8z95grym1y3zlvgjfv3q65i", 2146 "depends": ["BiocParallel", "SC3", "SingleCellExperiment", "SummarizedExperiment", "TSCAN", "irlba", "matrixStats", "mclust"] 2147 }, 2148 "FELLA": { 2149 "name": "FELLA", 2150 "version": "1.30.0", 2151 "sha256": "09ahamrbzai0pw7pkd9dxcray8ziqp4x7vl7makkpig1x9vsq10n", 2152 "depends": ["KEGGREST", "Matrix", "igraph", "plyr"] 2153 }, 2154 "FGNet": { 2155 "name": "FGNet", 2156 "version": "3.44.0", 2157 "sha256": "1g9r62pp4qcrmfc3g222p5rw8afap6m54k05j6bbasr8sx69m18g", 2158 "depends": ["RColorBrewer", "R_utils", "XML", "hwriter", "igraph", "plotrix", "png", "reshape2"] 2159 }, 2160 "FISHalyseR": { 2161 "name": "FISHalyseR", 2162 "version": "1.44.0", 2163 "sha256": "016agx3dci46srbb82lnyk42cxxia0in06hk9f9s6gai0rd7rqxn", 2164 "depends": ["EBImage", "abind"] 2165 }, 2166 "FLAMES": { 2167 "name": "FLAMES", 2168 "version": "2.4.0", 2169 "sha256": "0n0a8zlydmd03pd2ymdf5nafsc09y8glfgr31dag37y93xc7a9zs", 2170 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "ComplexHeatmap", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "RColorBrewer", "R_utils", "Rcpp", "Rhtslib", "Rsamtools", "S4Arrays", "S4Vectors", "Seqinfo", "ShortRead", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "abind", "bambu", "basilisk", "circlize", "cli", "cowplot", "crew", "dplyr", "ggbio", "ggplot2", "gridExtra", "igraph", "jsonlite", "magick", "magrittr", "readr", "reticulate", "rtracklayer", "scater", "scatterpie", "scran", "scuttle", "stringr", "testthat", "tibble", "tidyr", "tidyselect", "withr"] 2171 }, 2172 "FRASER": { 2173 "name": "FRASER", 2174 "version": "2.6.0", 2175 "sha256": "1h9j04q0b956kikwlwzfgn6amd4wf56ybqim3r6vikmhqacm94l7", 2176 "depends": ["AnnotationDbi", "BBmisc", "BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "DelayedArray", "DelayedMatrixStats", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "HDF5Array", "IRanges", "OUTRIDER", "PRROC", "RColorBrewer", "RMTstat", "R_utils", "Rcpp", "RcppArmadillo", "Rsamtools", "Rsubread", "S4Vectors", "SummarizedExperiment", "VGAM", "biomaRt", "cowplot", "data_table", "extraDistr", "generics", "ggplot2", "ggrepel", "matrixStats", "pcaMethods", "pheatmap", "plotly", "pracma", "rhdf5", "tibble"] 2177 }, 2178 "FRGEpistasis": { 2179 "name": "FRGEpistasis", 2180 "version": "1.46.0", 2181 "sha256": "18zjy8v0bjh0i9chmy390g70v33ni6flj1vfdanh3vrfbfk2m341", 2182 "depends": ["MASS", "fda"] 2183 }, 2184 "FamAgg": { 2185 "name": "FamAgg", 2186 "version": "1.38.0", 2187 "sha256": "0i6h2clwylxnxc4dwqggpq7y3cncp9qp4n7l8ypkl20kaq3s676a", 2188 "depends": ["BiocGenerics", "Matrix", "gap", "igraph", "kinship2", "survey"] 2189 }, 2190 "FastqCleaner": { 2191 "name": "FastqCleaner", 2192 "version": "1.28.0", 2193 "sha256": "1fdd89x18k00in855f11h6fj4m5kwkipanbf8zmrrnwkawm62cc1", 2194 "depends": ["Biostrings", "DT", "IRanges", "Rcpp", "S4Vectors", "ShortRead", "htmltools", "shiny", "shinyBS"] 2195 }, 2196 "FeatSeekR": { 2197 "name": "FeatSeekR", 2198 "version": "1.10.0", 2199 "sha256": "0akq90c0hb5gbl35lnql3crr00k3dmigs65phs9c1i22wa2qqlqr", 2200 "depends": ["MASS", "SummarizedExperiment", "pheatmap", "pracma"] 2201 }, 2202 "FilterFFPE": { 2203 "name": "FilterFFPE", 2204 "version": "1.20.0", 2205 "sha256": "11b46qwg6sq7q7vnq18pcnfpnjavs97azmg0034a214gg7f9kila", 2206 "depends": ["GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "doParallel", "foreach"] 2207 }, 2208 "FindIT2": { 2209 "name": "FindIT2", 2210 "version": "1.16.0", 2211 "sha256": "0ld9xvy1r8a27alf4w368x9yvmwx8fy43yv0izp39y1x1jpvkqj8", 2212 "depends": ["BiocGenerics", "BiocParallel", "GenomicFeatures", "GenomicRanges", "IRanges", "MultiAssayExperiment", "S4Vectors", "Seqinfo", "SummarizedExperiment", "dplyr", "ggplot2", "ggrepel", "glmnet", "patchwork", "progress", "purrr", "qvalue", "rlang", "rtracklayer", "stringr", "tibble", "tidyr", "withr"] 2213 }, 2214 "FinfoMDS": { 2215 "name": "FinfoMDS", 2216 "version": "1.0.0", 2217 "sha256": "0gr2vm0d0qkk6y8rdvyicf468d317ffdyzq7fdxcn5iv0dgci9wq", 2218 "depends": ["phyloseq"] 2219 }, 2220 "FitHiC": { 2221 "name": "FitHiC", 2222 "version": "1.36.0", 2223 "sha256": "1s454gpagdcj4gz5nbgvip3nw1kpp95bi6db9y302yrmpwds8vpq", 2224 "depends": ["Rcpp", "data_table", "fdrtool"] 2225 }, 2226 "FlowSOM": { 2227 "name": "FlowSOM", 2228 "version": "2.18.0", 2229 "sha256": "09a3s5aqp9kfvckf2mw8lj0q74b3wmbg1qnphrggdcilhhh107di", 2230 "depends": ["BiocGenerics", "ConsensusClusterPlus", "Rtsne", "XML", "colorRamps", "dplyr", "flowCore", "ggforce", "ggnewscale", "ggplot2", "ggpubr", "igraph", "magrittr", "rlang", "tidyr"] 2231 }, 2232 "FuseSOM": { 2233 "name": "FuseSOM", 2234 "version": "1.12.0", 2235 "sha256": "1wavm6njapw7p5jvalghg981wgbgfrqfqhx6aqyvv2r5q14rkkwp", 2236 "depends": ["FCPS", "Rcpp", "S4Vectors", "SummarizedExperiment", "analogue", "cluster", "coop", "diptest", "fastcluster", "fpc", "ggplot2", "ggplotify", "ggpubr", "pheatmap", "proxy", "psych", "stringr"] 2237 }, 2238 "G4SNVHunter": { 2239 "name": "G4SNVHunter", 2240 "version": "1.2.0", 2241 "sha256": "00zhnsnbz8c7nns2srapikwmrvp0vvf7mz3f881c6rxgvndhppc8", 2242 "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rcpp", "RcppRoll", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "cowplot", "data_table", "dplyr", "ggdensity", "ggplot2", "ggpointdensity", "ggseqlogo", "magrittr", "openxlsx", "progress", "tidyr", "viridis"] 2243 }, 2244 "GA4GHclient": { 2245 "name": "GA4GHclient", 2246 "version": "1.34.0", 2247 "sha256": "0w9bmfll450m4qrl984bzrjb8rnzr08z3zgkvbi7g2yf3dv1jg6q", 2248 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "VariantAnnotation", "dplyr", "httr", "jsonlite"] 2249 }, 2250 "GA4GHshiny": { 2251 "name": "GA4GHshiny", 2252 "version": "1.32.0", 2253 "sha256": "00im5cspwvnks9dns9ncbzi8fv6q127yc58lfr3qsxgxbm6li017", 2254 "depends": ["AnnotationDbi", "BiocGenerics", "DT", "GA4GHclient", "GenomeInfoDb", "GenomicFeatures", "S4Vectors", "Seqinfo", "dplyr", "openxlsx", "purrr", "shiny", "shinyjs", "shinythemes", "tidyr"] 2255 }, 2256 "GARS": { 2257 "name": "GARS", 2258 "version": "1.30.0", 2259 "sha256": "1kzmi8w91f976x7c7l4aj7qy2xydspphaggdgcylmkvh8d464kyp", 2260 "depends": ["DaMiRseq", "MLSeq", "SummarizedExperiment", "cluster", "ggplot2"] 2261 }, 2262 "GAprediction": { 2263 "name": "GAprediction", 2264 "version": "1.36.0", 2265 "sha256": "10yxp3kkx7ky87q17n3n9dja8af6c61pmz25zrj74xkip43qhkna", 2266 "depends": ["Matrix", "glmnet"] 2267 }, 2268 "GBScleanR": { 2269 "name": "GBScleanR", 2270 "version": "2.3.2", 2271 "sha256": "0pb85ybypa0i5dnqv0ywffdkp53l1knv512dc2a2z9kmjifg4l3l", 2272 "depends": ["Rcpp", "RcppParallel", "SeqArray", "expm", "gdsfmt", "ggplot2", "tidyr"] 2273 }, 2274 "GCPtools": { 2275 "name": "GCPtools", 2276 "version": "1.0.0", 2277 "sha256": "1m4ljd33vg5ari4xq8x1qsmdp0232w8f7x140mdh1gvg545rjjf4", 2278 "depends": ["AnVILBase", "BiocBaseUtils", "dplyr", "httr", "rlang", "tibble", "tidyr"] 2279 }, 2280 "GDCRNATools": { 2281 "name": "GDCRNATools", 2282 "version": "1.30.0", 2283 "sha256": "12za6x6im4cpdk2g9w2d6smj0hxbn7v43h4dxq9c6sm5hyn6fv3i", 2284 "depends": ["BiocParallel", "DESeq2", "DOSE", "DT", "GenomicDataCommons", "XML", "biomaRt", "clusterProfiler", "edgeR", "ggplot2", "gplots", "jsonlite", "limma", "org_Hs_eg_db", "pathview", "rjson", "shiny", "survival", "survminer"] 2285 }, 2286 "GDSArray": { 2287 "name": "GDSArray", 2288 "version": "1.30.0", 2289 "sha256": "1cvpk3x7yh08dblndf963alz9wc8crfzy271hxiz143gwmgfhn36", 2290 "depends": ["BiocGenerics", "DelayedArray", "S4Vectors", "SNPRelate", "SeqArray", "gdsfmt"] 2291 }, 2292 "GEM": { 2293 "name": "GEM", 2294 "version": "1.36.0", 2295 "sha256": "0dx4ldbhc7w2h599sd5mcsvj45m9i3xzm9vh1m0j1wa079gfmk14", 2296 "depends": ["ggplot2"] 2297 }, 2298 "GENESIS": { 2299 "name": "GENESIS", 2300 "version": "2.40.0", 2301 "sha256": "1g0cilgak0538wlq35m187d6mi3byfb44kic230idmi13ybq2yjw", 2302 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "GWASTools", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SNPRelate", "SeqArray", "SeqVarTools", "data_table", "gdsfmt", "igraph", "reshape2"] 2303 }, 2304 "GENIE3": { 2305 "name": "GENIE3", 2306 "version": "1.32.0", 2307 "sha256": "0q48p119hg7x8w6m4xv0s9h6ii8334hq4dl32b4ffbdlmi41kia9", 2308 "depends": ["dplyr", "reshape2"] 2309 }, 2310 "GEOfastq": { 2311 "name": "GEOfastq", 2312 "version": "1.18.0", 2313 "sha256": "132aky7zffvhzfnazvl8i3y82vvpipvm3kgdppbpjjiig4l3cz0q", 2314 "depends": ["RCurl", "doParallel", "foreach", "plyr", "rvest", "stringr", "xml2"] 2315 }, 2316 "GEOmetadb": { 2317 "name": "GEOmetadb", 2318 "version": "1.72.0", 2319 "sha256": "0fhmcawv1lvbmkmfzyk0q83rcmiyc3m9visp4904nllv94zb4ir1", 2320 "depends": ["RSQLite", "R_utils"] 2321 }, 2322 "GEOquery": { 2323 "name": "GEOquery", 2324 "version": "2.78.0", 2325 "sha256": "1rvvfyg7qz9sd02ymfs6006dmdm200aryliripnqkm6cdjzxd4mp", 2326 "depends": ["Biobase", "R_utils", "S4Vectors", "SummarizedExperiment", "curl", "data_table", "dplyr", "httr2", "limma", "magrittr", "readr", "rentrez", "rvest", "stringr", "tidyr", "xml2"] 2327 }, 2328 "GEOsubmission": { 2329 "name": "GEOsubmission", 2330 "version": "1.62.0", 2331 "sha256": "1b2yx94ybc3rnbbwf7d70wbgq908k81xr9sbwb0aswjrsx551vfp", 2332 "depends": ["Biobase", "affy"] 2333 }, 2334 "GEWIST": { 2335 "name": "GEWIST", 2336 "version": "1.54.0", 2337 "sha256": "12wj9f2lgacb157lzw9mn7d7nzy6kyiqzxrgkv0rj9lq5ng26bv8", 2338 "depends": ["car"] 2339 }, 2340 "GGPA": { 2341 "name": "GGPA", 2342 "version": "1.22.0", 2343 "sha256": "0lqrxf0qshcn7gkhil0qsmf65n1aa52z5pxlayr28rwkn8sjllr4", 2344 "depends": ["GGally", "Rcpp", "RcppArmadillo", "matrixStats", "network", "scales", "sna"] 2345 }, 2346 "GIGSEA": { 2347 "name": "GIGSEA", 2348 "version": "1.28.0", 2349 "sha256": "043ncc99w8a7pj04n17vcwrdq02f2636xqwcifrfaa0q7p0ir93w", 2350 "depends": ["MASS", "Matrix", "locfdr"] 2351 }, 2352 "GLAD": { 2353 "name": "GLAD", 2354 "version": "2.74.0", 2355 "sha256": "1gqkr7bp8rrad8dq7jcmdda6604vnqg781wx7adpndwss0xi1zyh", 2356 "depends": ["aws"] 2357 }, 2358 "GMRP": { 2359 "name": "GMRP", 2360 "version": "1.38.0", 2361 "sha256": "0xmf2rppnnn6lgxv1d88y52prqms2cryq31v4n9d3pvjk1899igj", 2362 "depends": ["GenomicRanges", "diagram", "plotrix"] 2363 }, 2364 "GNET2": { 2365 "name": "GNET2", 2366 "version": "1.26.0", 2367 "sha256": "1s4iy7dwb82hgi08a08pjhmm29r4jhd8anbk11p15fax1pc3xhq9", 2368 "depends": ["DiagrammeR", "Rcpp", "SummarizedExperiment", "dplyr", "ggplot2", "igraph", "matrixStats", "reshape2", "xgboost"] 2369 }, 2370 "GNOSIS": { 2371 "name": "GNOSIS", 2372 "version": "1.8.0", 2373 "sha256": "1m6p557jgwyr6ccglccw7ryxnkgalb18aralbmclmdfp6k65npfq", 2374 "depends": ["DT", "DescTools", "RColorBrewer", "cBioPortalData", "car", "compareGroups", "dashboardthemes", "fabricatr", "fontawesome", "maftools", "magrittr", "operator_tools", "partykit", "reshape2", "rpart", "rstatix", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinydashboardPlus", "shinyjs", "shinylogs", "shinymeta", "survival", "survminer", "tidyverse"] 2375 }, 2376 "GOSemSim": { 2377 "name": "GOSemSim", 2378 "version": "2.36.0", 2379 "sha256": "0s5zpga9fjk5h8l8ql8zpyylqrfqfgy8zw9i60mlr8azifwq7hvk", 2380 "depends": ["AnnotationDbi", "DBI", "GO_db", "R_utils", "Rcpp", "digest", "rlang", "yulab_utils"] 2381 }, 2382 "GOTHiC": { 2383 "name": "GOTHiC", 2384 "version": "1.46.0", 2385 "sha256": "0wvzzyff1v57sdj6dd7423gya9vrrfkhwmw8129dr0zsfvk9qwwr", 2386 "depends": ["BSgenome", "BiocGenerics", "BiocManager", "Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "ShortRead", "data_table", "ggplot2", "rtracklayer"] 2387 }, 2388 "GOexpress": { 2389 "name": "GOexpress", 2390 "version": "1.44.0", 2391 "sha256": "0kdlqvgssakc67pgc39p3qbyhc43x9gmi3vyrjn97h37i49f0mhr", 2392 "depends": ["Biobase", "RColorBrewer", "RCurl", "biomaRt", "ggplot2", "gplots", "randomForest", "stringr"] 2393 }, 2394 "GOfuncR": { 2395 "name": "GOfuncR", 2396 "version": "1.30.0", 2397 "sha256": "1rvvzj3maa6xvvs0r9l994zk5pjbxgfmflg8waqqm6d6rd4ls4dv", 2398 "depends": ["AnnotationDbi", "GenomicRanges", "IRanges", "Rcpp", "gtools", "mapplots", "vioplot"] 2399 }, 2400 "GOpro": { 2401 "name": "GOpro", 2402 "version": "1.36.0", 2403 "sha256": "0ry7h5gzzbyfi74m33qvqb8v8fj0y16ysf3wfnjhf9jngj365856", 2404 "depends": ["AnnotationDbi", "BH", "GO_db", "IRanges", "MultiAssayExperiment", "Rcpp", "S4Vectors", "dendextend", "doParallel", "foreach", "org_Hs_eg_db"] 2405 }, 2406 "GOstats": { 2407 "name": "GOstats", 2408 "version": "2.76.0", 2409 "sha256": "1424z2hgimhwhwbwzz82vdsrgcwyfacn4mxl26ms2mry5mff9m9g", 2410 "depends": ["AnnotationDbi", "AnnotationForge", "Biobase", "Category", "GO_db", "RBGL", "Rgraphviz", "annotate", "graph"] 2411 }, 2412 "GPA": { 2413 "name": "GPA", 2414 "version": "1.22.0", 2415 "sha256": "0w8mgcx1yiixa81s8yavka7q5kaly3fm9vvbp4jnx7d3mv8r74nr", 2416 "depends": ["DT", "Rcpp", "ggplot2", "ggrepel", "plyr", "shiny", "shinyBS", "vegan"] 2417 }, 2418 "GRENITS": { 2419 "name": "GRENITS", 2420 "version": "1.62.0", 2421 "sha256": "18hjfsx4a8fyv458l71q0hz0k1jg07g0nkfh2v80vk7plkplqz7k", 2422 "depends": ["Rcpp", "RcppArmadillo", "ggplot2", "reshape2"] 2423 }, 2424 "GRaNIE": { 2425 "name": "GRaNIE", 2426 "version": "1.14.0", 2427 "sha256": "16alzawsgk7a6jn6vc3jj4csh9l97z9nsh4i4x2g1nm5wx5sq8ry", 2428 "depends": ["AnnotationHub", "Biostrings", "ComplexHeatmap", "DESeq2", "GenomeInfoDb", "GenomicRanges", "Matrix", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "biomaRt", "checkmate", "circlize", "colorspace", "data_table", "dplyr", "ensembldb", "forcats", "futile_logger", "ggplot2", "gridExtra", "igraph", "limma", "magrittr", "matrixStats", "patchwork", "progress", "readr", "reshape2", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect", "topGO", "viridis"] 2429 }, 2430 "GRmetrics": { 2431 "name": "GRmetrics", 2432 "version": "1.36.0", 2433 "sha256": "1irgiwfx6s7w413mgdidkn341qhxqn050bdmh4mf3bh3dpmlrqij", 2434 "depends": ["S4Vectors", "SummarizedExperiment", "drc", "ggplot2", "plotly"] 2435 }, 2436 "GSALightning": { 2437 "name": "GSALightning", 2438 "version": "1.38.0", 2439 "sha256": "16sm2sa4jvwpcd0hndg5khi4lzrsywjk05qfa05l19lgxfrcyfss", 2440 "depends": ["Matrix", "data_table"] 2441 }, 2442 "GSAR": { 2443 "name": "GSAR", 2444 "version": "1.44.0", 2445 "sha256": "0p190i2kqzz0515phsj8hp83h8bix2hw0lwy7li2ghm4p85lf51k", 2446 "depends": ["igraph"] 2447 }, 2448 "GSCA": { 2449 "name": "GSCA", 2450 "version": "2.40.0", 2451 "sha256": "1d6c9lxri0j5j84yn0fhdqv7ddhgpa8j0ypf3blvq3afl2jm0rjj", 2452 "depends": ["RColorBrewer", "ggplot2", "gplots", "reshape2", "rhdf5", "shiny", "sp"] 2453 }, 2454 "GSEABase": { 2455 "name": "GSEABase", 2456 "version": "1.72.0", 2457 "sha256": "1sxd159msf51x1wfd2v67ngbc0lj6a8vdrc027f1xryh4gnnryk9", 2458 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "XML", "annotate", "graph"] 2459 }, 2460 "GSEABenchmarkeR": { 2461 "name": "GSEABenchmarkeR", 2462 "version": "1.30.0", 2463 "sha256": "0absc89fkhg1szjlc7brcw4nyvilp8w5h6yxq6gw1gx7z5k47gka", 2464 "depends": ["AnnotationDbi", "AnnotationHub", "Biobase", "BiocFileCache", "BiocParallel", "EnrichmentBrowser", "ExperimentHub", "KEGGandMetacoreDzPathwaysGEO", "KEGGdzPathwaysGEO", "S4Vectors", "SummarizedExperiment", "edgeR"] 2465 }, 2466 "GSEAlm": { 2467 "name": "GSEAlm", 2468 "version": "1.70.0", 2469 "sha256": "0p29pvg0aaxarnlhr027031d191djscy2cl621rml40nd5dw5dyg", 2470 "depends": ["Biobase"] 2471 }, 2472 "GSEAmining": { 2473 "name": "GSEAmining", 2474 "version": "1.20.0", 2475 "sha256": "1bljvni74vpbdf8n9b7yhh4r2wd4wr84rabinl8cr35jgipj1agv", 2476 "depends": ["dendextend", "dplyr", "ggplot2", "ggwordcloud", "gridExtra", "rlang", "stringr", "tibble", "tidytext"] 2477 }, 2478 "GSRI": { 2479 "name": "GSRI", 2480 "version": "2.58.0", 2481 "sha256": "0j7vb5j9f3mdi42wap6qz2zd07aaymggw8sa7d7fj9inpr8jj2py", 2482 "depends": ["Biobase", "GSEABase", "fdrtool", "genefilter", "les"] 2483 }, 2484 "GSReg": { 2485 "name": "GSReg", 2486 "version": "1.44.0", 2487 "sha256": "0f88hz0mqbp4pxgh7hwjav3dcjf2qw1gpfabziqdprm3xpkkfqc2", 2488 "depends": ["AnnotationDbi", "GenomicFeatures", "Homo_sapiens", "org_Hs_eg_db"] 2489 }, 2490 "GSVA": { 2491 "name": "GSVA", 2492 "version": "2.4.0", 2493 "sha256": "169kikbzb5afgclcm73jgnrp2h6g5i9sckw2zkjjj797pc6vd1jz", 2494 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "GSEABase", "HDF5Array", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "SummarizedExperiment", "cli", "sparseMatrixStats"] 2495 }, 2496 "GSgalgoR": { 2497 "name": "GSgalgoR", 2498 "version": "1.20.0", 2499 "sha256": "1544lnv9jkcwdc7056dydpmydpkgyphv7pfyqd2wria13rm0vg2c", 2500 "depends": ["cluster", "doParallel", "foreach", "matchingR", "nsga2R", "proxy", "survival"] 2501 }, 2502 "GUIDEseq": { 2503 "name": "GUIDEseq", 2504 "version": "1.40.0", 2505 "sha256": "1nm7bfg6s68m1p4il60cm0p1sfy9lqswispd1mlcbfmlqj7n7b74", 2506 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "CRISPRseek", "ChIPpeakAnno", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "data_table", "dplyr", "ggplot2", "hash", "limma", "matrixStats", "multtest", "openxlsx", "patchwork", "purrr", "pwalign", "rio", "rlang", "stringr", "tidyr"] 2507 }, 2508 "GWAS_BAYES": { 2509 "name": "GWAS.BAYES", 2510 "version": "1.20.0", 2511 "sha256": "17q782b4qfs471vc8ivg64ika97698swramclfrqbhpk7444xq9k", 2512 "depends": ["GA", "MASS", "Matrix", "caret", "limma", "memoise"] 2513 }, 2514 "GWASTools": { 2515 "name": "GWASTools", 2516 "version": "1.56.0", 2517 "sha256": "0lkv2ccibjh7mw3p4j17ir5c0kp96q6086wh6h9ida33mbbbjw7k", 2518 "depends": ["Biobase", "DBI", "DNAcopy", "GWASExactHW", "RSQLite", "data_table", "gdsfmt", "lmtest", "logistf", "quantsmooth", "sandwich", "survival"] 2519 }, 2520 "GWENA": { 2521 "name": "GWENA", 2522 "version": "1.20.0", 2523 "sha256": "119ap7kdi9vrxi6v7rh7wmkfabz985jizjxhnnk2wc6crd3sajms", 2524 "depends": ["NetRep", "RColorBrewer", "SummarizedExperiment", "WGCNA", "cluster", "dplyr", "dynamicTreeCut", "ggplot2", "gprofiler2", "igraph", "magrittr", "matrixStats", "purrr", "rlist", "stringr", "tibble", "tidyr"] 2525 }, 2526 "GateFinder": { 2527 "name": "GateFinder", 2528 "version": "1.30.0", 2529 "sha256": "0g0j96r0a1c4l2ns5cmvr8b1pdf6ph37mswbkjc25wdkykim1f5x", 2530 "depends": ["diptest", "flowCore", "flowFP", "mvoutlier", "splancs"] 2531 }, 2532 "GenProSeq": { 2533 "name": "GenProSeq", 2534 "version": "1.14.0", 2535 "sha256": "1mrbj0adlvngchyk8jhqsykhwawhmq4sxybmj3nwi4zgr3ad9781", 2536 "depends": ["CatEncoders", "DeepPINCS", "keras", "mclust", "reticulate", "tensorflow", "ttgsea", "word2vec"] 2537 }, 2538 "GeneBreak": { 2539 "name": "GeneBreak", 2540 "version": "1.40.0", 2541 "sha256": "0s4973b63rdcdci9gm6rp19rjd1zsknfyi7sp81jb3d0b3jgxhnj", 2542 "depends": ["CGHbase", "CGHcall", "GenomicRanges", "QDNAseq"] 2543 }, 2544 "GeneExpressionSignature": { 2545 "name": "GeneExpressionSignature", 2546 "version": "1.56.0", 2547 "sha256": "0rzi04xbqhbyk1l9vcndd0abhi0qa58bgn5bdb214lphf9p2rp1k", 2548 "depends": ["Biobase"] 2549 }, 2550 "GeneGA": { 2551 "name": "GeneGA", 2552 "version": "1.60.0", 2553 "sha256": "1ifni019hlsvf68ksm31fj0pn1455j22vq00c1368cjmnysbvclk", 2554 "depends": ["hash", "seqinr"] 2555 }, 2556 "GeneMeta": { 2557 "name": "GeneMeta", 2558 "version": "1.82.0", 2559 "sha256": "18b5zkji6k6vaw42amhimkxnijrk3vff6bn3kyx9fvx70czv6yp3", 2560 "depends": ["Biobase", "genefilter"] 2561 }, 2562 "GeneNetworkBuilder": { 2563 "name": "GeneNetworkBuilder", 2564 "version": "1.52.0", 2565 "sha256": "1l439fyqg49sz8c00h225xlc9jdd017bvhagws69hfadms2qlvca", 2566 "depends": ["RCy3", "Rcpp", "Rgraphviz", "XML", "graph", "htmlwidgets", "plyr", "rjson"] 2567 }, 2568 "GeneOverlap": { 2569 "name": "GeneOverlap", 2570 "version": "1.46.0", 2571 "sha256": "05yf6h1swvmfgn5zkjrlq7w8kxyidi4nqygw0d65plkb655b6wav", 2572 "depends": ["RColorBrewer", "gplots"] 2573 }, 2574 "GeneRegionScan": { 2575 "name": "GeneRegionScan", 2576 "version": "1.66.0", 2577 "sha256": "1m7a9sxaa9m7axn79l965p2bvqa0pfjr2az0mff1gqaw7b9pvbh2", 2578 "depends": ["Biobase", "Biostrings", "RColorBrewer", "S4Vectors", "affxparser"] 2579 }, 2580 "GeneSelectMMD": { 2581 "name": "GeneSelectMMD", 2582 "version": "2.54.0", 2583 "sha256": "10xfc6cql49f5s169pmfnh82fgmwjvlmabq5bdrhzmpa3a5n5xzw", 2584 "depends": ["Biobase", "MASS", "limma"] 2585 }, 2586 "GeneStructureTools": { 2587 "name": "GeneStructureTools", 2588 "version": "1.30.0", 2589 "sha256": "09wbbhrmvq3zxvx9xa087w5v17y8m5kn998bl0v1kbwlms0pnqf6", 2590 "depends": ["BSgenome_Mmusculus_UCSC_mm10", "Biostrings", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "data_table", "plyr", "rtracklayer", "stringdist", "stringr"] 2591 }, 2592 "GeneticsPed": { 2593 "name": "GeneticsPed", 2594 "version": "1.72.0", 2595 "sha256": "0zx48p90k3kdjvz0aasr0zn2288c1wqzrs6s5p1npc7ddcx0wy98", 2596 "depends": ["MASS", "gdata", "genetics"] 2597 }, 2598 "GenomAutomorphism": { 2599 "name": "GenomAutomorphism", 2600 "version": "1.12.0", 2601 "sha256": "190alhczdvhyq0rj94h3nwcp33hpw4r6hm9rgan2l2jak5yr6fwh", 2602 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "XVector", "data_table", "doParallel", "dplyr", "foreach", "matrixStats", "numbers"] 2603 }, 2604 "GenomeInfoDb": { 2605 "name": "GenomeInfoDb", 2606 "version": "1.46.0", 2607 "sha256": "03mxzpz9pwhmg63is4pn5gbrkcphfj9nyzdpxymhy9s8nv3hzfd9", 2608 "depends": ["BiocGenerics", "IRanges", "S4Vectors", "Seqinfo", "UCSC_utils"] 2609 }, 2610 "GenomicAlignments": { 2611 "name": "GenomicAlignments", 2612 "version": "1.46.0", 2613 "sha256": "18s65wfkb568fiqqxbg50qpjv2x1ryrj3zrmafqqsp7xv6da6zzj", 2614 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "cigarillo"] 2615 }, 2616 "GenomicDataCommons": { 2617 "name": "GenomicDataCommons", 2618 "version": "1.33.1", 2619 "sha256": "0x4h82rqjiicxb1kfbg4a43yi620nrw3msw2vgfys7pyl1cmh3is", 2620 "depends": ["GenomicRanges", "IRanges", "dplyr", "httr", "jsonlite", "rappdirs", "readr", "rlang", "tibble", "tidyr", "xml2"] 2621 }, 2622 "GenomicDistributions": { 2623 "name": "GenomicDistributions", 2624 "version": "1.18.0", 2625 "sha256": "18ifnqsh95yhc990bi4dnr9fd0hbr7jksvpwlxvh6am3lsrg9b8s", 2626 "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "broom", "data_table", "dplyr", "ggplot2", "plyr", "reshape2", "scales"] 2627 }, 2628 "GenomicFeatures": { 2629 "name": "GenomicFeatures", 2630 "version": "1.62.0", 2631 "sha256": "0rszhpmfsvn5iz3gzr3z07r7ykpmk4cbmfnjf9k2z59knnn1x9gp", 2632 "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "DBI", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "XVector", "rtracklayer"] 2633 }, 2634 "GenomicFiles": { 2635 "name": "GenomicFiles", 2636 "version": "1.46.0", 2637 "sha256": "0mw8h491i20lq94r4dd4ky7ivn7ci722g314rdaphm2dvknkrda7", 2638 "depends": ["BiocBaseUtils", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MatrixGenerics", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "rtracklayer"] 2639 }, 2640 "GenomicInteractionNodes": { 2641 "name": "GenomicInteractionNodes", 2642 "version": "1.14.0", 2643 "sha256": "1fwl85smbprr7gdhgrwnr8dp0hr0xk5xqsycdzzi592nf1vz6imy", 2644 "depends": ["AnnotationDbi", "GO_db", "GenomicFeatures", "GenomicRanges", "IRanges", "RBGL", "S4Vectors", "Seqinfo", "graph"] 2645 }, 2646 "GenomicInteractions": { 2647 "name": "GenomicInteractions", 2648 "version": "1.44.0", 2649 "sha256": "1kfmlznlagjxzvwpnk18b5f5612fflkm66m93gky6ppi65ppv7xp", 2650 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "InteractionSet", "Rsamtools", "S4Vectors", "Seqinfo", "data_table", "dplyr", "ggplot2", "gridExtra", "igraph", "rtracklayer", "stringr"] 2651 }, 2652 "GenomicOZone": { 2653 "name": "GenomicOZone", 2654 "version": "1.24.0", 2655 "sha256": "13m5h8ychama0bg52mnd73yq3g3zp3mh445y9q9hc8pbwr6ybxiw", 2656 "depends": ["Ckmeans_1d_dp", "GenomicRanges", "IRanges", "Rdpack", "S4Vectors", "Seqinfo", "biomaRt", "ggbio", "ggplot2", "gridExtra", "lsr", "plyr"] 2657 }, 2658 "GenomicPlot": { 2659 "name": "GenomicPlot", 2660 "version": "1.8.0", 2661 "sha256": "0nb1jl5fv2jn9mza0qxysczp5zas0xy3h61kmfjxkivqdnn0ga5b", 2662 "depends": ["BiocGenerics", "ComplexHeatmap", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RCAS", "Rsamtools", "Seqinfo", "VennDiagram", "circlize", "cowplot", "dplyr", "edgeR", "genomation", "ggplot2", "ggplotify", "ggpubr", "ggsci", "ggsignif", "plyranges", "rtracklayer", "scales", "tidyr", "txdbmaker", "viridis"] 2663 }, 2664 "GenomicRanges": { 2665 "name": "GenomicRanges", 2666 "version": "1.62.0", 2667 "sha256": "0wsbl49c542k107cgczsw5dynnrrwk9hslks229zpvxlcvapmivv", 2668 "depends": ["BiocGenerics", "IRanges", "S4Vectors", "Seqinfo"] 2669 }, 2670 "GenomicScores": { 2671 "name": "GenomicScores", 2672 "version": "2.22.0", 2673 "sha256": "02ij02npfcx97bapga1w3mfy7k6fkf203gsd5b5rf19ja79bq4nw", 2674 "depends": ["AnnotationHub", "Biobase", "BiocFileCache", "BiocGenerics", "BiocManager", "Biostrings", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "S4Vectors", "Seqinfo", "XML", "httr", "rhdf5"] 2675 }, 2676 "GenomicSuperSignature": { 2677 "name": "GenomicSuperSignature", 2678 "version": "1.18.0", 2679 "sha256": "04dmmmgzmzkwdrydg4a3wv0zna4imiv8by4fbs776gpas1cbpag0", 2680 "depends": ["Biobase", "BiocFileCache", "ComplexHeatmap", "S4Vectors", "SummarizedExperiment", "dplyr", "flextable", "ggplot2", "ggpubr", "irlba", "plotly"] 2681 }, 2682 "GenomicTuples": { 2683 "name": "GenomicTuples", 2684 "version": "1.44.0", 2685 "sha256": "0c9b0vvwzm99qfx36nlz1b4nvnsjirdh22121w0wnsrn0x2xi398", 2686 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors", "Seqinfo", "data_table"] 2687 }, 2688 "GeoDiff": { 2689 "name": "GeoDiff", 2690 "version": "1.16.0", 2691 "sha256": "04jmzrz0y1yq6hqzvqp7wyv489xxswr2rv9ag4fvdcmgkzwikwnk", 2692 "depends": ["Biobase", "GeomxTools", "Matrix", "NanoStringNCTools", "Rcpp", "RcppArmadillo", "lme4", "plyr", "robust", "roptim", "testthat", "withr"] 2693 }, 2694 "GeoTcgaData": { 2695 "name": "GeoTcgaData", 2696 "version": "2.10.0", 2697 "sha256": "1rkyzq2i4rk2rhppbzqppkgl2886fhkkzb7i6xyn4zmajw7jq2vk", 2698 "depends": ["SummarizedExperiment", "cqn", "data_table", "plyr", "topconfects"] 2699 }, 2700 "GeomxTools": { 2701 "name": "GeomxTools", 2702 "version": "3.14.0", 2703 "sha256": "0i0dy14vchh53nsfdhslgkmcc64yiip6kj2mjsfmcyjffr8jwn8b", 2704 "depends": ["Biobase", "BiocGenerics", "EnvStats", "GGally", "NanoStringNCTools", "S4Vectors", "SeuratObject", "data_table", "dplyr", "ggplot2", "lmerTest", "readxl", "reshape2", "rjson", "rlang", "stringr"] 2705 }, 2706 "GladiaTOX": { 2707 "name": "GladiaTOX", 2708 "version": "1.26.0", 2709 "sha256": "1ij5kqkm21da1193h5rq7ahif6rfsrgnv446l2cx9nlc1rfss99a", 2710 "depends": ["DBI", "RColorBrewer", "RCurl", "RJSONIO", "RMariaDB", "RSQLite", "XML", "brew", "data_table", "ggplot2", "ggrepel", "numDeriv", "stringr", "tidyr", "xtable"] 2711 }, 2712 "Glimma": { 2713 "name": "Glimma", 2714 "version": "2.20.0", 2715 "sha256": "1icnw7f77vcgg4bk6scxg5qgcdhgy5kij38l3gxrm75gbp6xr23y", 2716 "depends": ["DESeq2", "S4Vectors", "SummarizedExperiment", "edgeR", "htmlwidgets", "jsonlite", "limma"] 2717 }, 2718 "GloScope": { 2719 "name": "GloScope", 2720 "version": "2.0.0", 2721 "sha256": "0vkvy3kmkmwg9g003cjhlczchqj1pxmlfp8y93hhxbwv4i6hxwzd", 2722 "depends": ["BiocParallel", "FNN", "MASS", "RANN", "RColorBrewer", "SingleCellExperiment", "boot", "cluster", "ggplot2", "mclust", "mvnfast", "permute", "pheatmap", "rlang", "vegan"] 2723 }, 2724 "GlobalAncova": { 2725 "name": "GlobalAncova", 2726 "version": "4.28.0", 2727 "sha256": "0r99pdfbvhfwlikz3lvz31q7xdfw7a51x9vwn79b2wwjkg36r6y8", 2728 "depends": ["AnnotationDbi", "Biobase", "GSEABase", "VGAM", "annotate", "corpcor", "dendextend", "globaltest"] 2729 }, 2730 "GmicR": { 2731 "name": "GmicR", 2732 "version": "1.24.0", 2733 "sha256": "0zr05hzcqy8wz75zw0q6j5jnzcrbwllsiq8l3yhk2biyi85xi3l4", 2734 "depends": ["AnnotationDbi", "Category", "DT", "GOstats", "GSEABase", "WGCNA", "ape", "bnlearn", "data_table", "doParallel", "foreach", "gRain", "gRbase", "org_Hs_eg_db", "org_Mm_eg_db", "reshape2", "shiny"] 2735 }, 2736 "GrafGen": { 2737 "name": "GrafGen", 2738 "version": "1.6.0", 2739 "sha256": "1lamgbykja2hjqvqbgkav9flbhlj6235afnda9w908x4zywi4hwc", 2740 "depends": ["GenomicRanges", "RColorBrewer", "cowplot", "dplyr", "ggplot2", "ggpubr", "plotly", "rlang", "scales", "shiny", "stringr"] 2741 }, 2742 "GraphAT": { 2743 "name": "GraphAT", 2744 "version": "1.82.0", 2745 "sha256": "114zcxv9fq6ljhn6wqra99ls5in7dqz942s2d4rk8ls2w92nnfjc", 2746 "depends": ["MCMCpack", "graph"] 2747 }, 2748 "GraphAlignment": { 2749 "name": "GraphAlignment", 2750 "version": "1.74.0", 2751 "sha256": "11dikrddkhgysi0528sn6qr7mmwwks1rdzyjygnbb1kyacf5m4bc", 2752 "depends": [] 2753 }, 2754 "GreyListChIP": { 2755 "name": "GreyListChIP", 2756 "version": "1.42.0", 2757 "sha256": "0gm1d021ik5k9dnvczagxdsrpfl85p4qzhbp1frar31ki15h3hli", 2758 "depends": ["BSgenome", "GenomicAlignments", "GenomicRanges", "MASS", "Rsamtools", "Seqinfo", "SummarizedExperiment", "rtracklayer"] 2759 }, 2760 "Guitar": { 2761 "name": "Guitar", 2762 "version": "2.26.0", 2763 "sha256": "02lhisr6ical6yy7m7r4w3b4nfxy5dhfydkaqh2fhfr4rd3igw0v", 2764 "depends": ["AnnotationDbi", "GenomicFeatures", "GenomicRanges", "dplyr", "ggplot2", "knitr", "magrittr", "rtracklayer"] 2765 }, 2766 "Gviz": { 2767 "name": "Gviz", 2768 "version": "1.54.0", 2769 "sha256": "0vljk50i5xgw31dgdxdjqxl2r3cvjm6423fz3iz80xbbax039mjs", 2770 "depends": ["AnnotationDbi", "BSgenome", "Biobase", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "XVector", "biomaRt", "biovizBase", "digest", "ensembldb", "lattice", "latticeExtra", "matrixStats", "rtracklayer"] 2771 }, 2772 "HDF5Array": { 2773 "name": "HDF5Array", 2774 "version": "1.38.0", 2775 "sha256": "1qk3qpy3lha44h0d7xr30qvp9gvxh1xr8xqz34irnq8c758zlcmp", 2776 "depends": ["BiocGenerics", "DelayedArray", "IRanges", "Matrix", "S4Arrays", "S4Vectors", "SparseArray", "h5mread", "rhdf5"] 2777 }, 2778 "HDTD": { 2779 "name": "HDTD", 2780 "version": "1.44.0", 2781 "sha256": "1qhvsrd50vxs16kkx0a60sb1jab88wnshi288n78dq8iz5kv52n4", 2782 "depends": ["Rcpp", "RcppArmadillo"] 2783 }, 2784 "HELP": { 2785 "name": "HELP", 2786 "version": "1.68.0", 2787 "sha256": "1n0c5s2pr1xqr0amsaf6ibdria0hpk7aavw5x74j5h2lgy438irh", 2788 "depends": ["Biobase"] 2789 }, 2790 "HEM": { 2791 "name": "HEM", 2792 "version": "1.82.0", 2793 "sha256": "0c78k48znjj9h5hbb4q8pamdjddcq7xpkc4isgvf6lr7ih9p26ka", 2794 "depends": ["Biobase"] 2795 }, 2796 "HERON": { 2797 "name": "HERON", 2798 "version": "1.8.0", 2799 "sha256": "1s46g0l2yj7kxqw9bm0xj0ymxbbjhr2yq9zflapn5a0acnn764zv", 2800 "depends": ["GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "cluster", "data_table", "harmonicmeanp", "limma", "matrixStats", "metap", "spdep"] 2801 }, 2802 "HGC": { 2803 "name": "HGC", 2804 "version": "1.18.0", 2805 "sha256": "11ywqqpmfmjqasmzryqcqhrfsjd4whicxy0bcigy18g1fwr1aj83", 2806 "depends": ["Matrix", "RANN", "Rcpp", "RcppEigen", "ape", "dendextend", "dplyr", "ggplot2", "mclust", "patchwork"] 2807 }, 2808 "HIBAG": { 2809 "name": "HIBAG", 2810 "version": "1.46.0", 2811 "sha256": "1qwq7z1b9w9fpaqwvizgzhlh1x1sb71frb5lmapa07v7vd2ma9l0", 2812 "depends": ["RcppParallel"] 2813 }, 2814 "HIPPO": { 2815 "name": "HIPPO", 2816 "version": "1.22.0", 2817 "sha256": "19yhqi6558nkr7z7acpnz5ssbdwq40jaiklgmkrggp0ajgqzwgjj", 2818 "depends": ["Matrix", "Rtsne", "SingleCellExperiment", "dplyr", "ggplot2", "ggrepel", "gridExtra", "irlba", "magrittr", "reshape2", "rlang", "umap"] 2819 }, 2820 "HIREewas": { 2821 "name": "HIREewas", 2822 "version": "1.28.0", 2823 "sha256": "15s30lyw9nj63iar93pad6ciccb0ak1iyhpvdj14hc8j03gbgplh", 2824 "depends": ["gplots", "quadprog"] 2825 }, 2826 "HMMcopy": { 2827 "name": "HMMcopy", 2828 "version": "1.52.0", 2829 "sha256": "1crn45v9mfciw54vmh80zaqwmxky23ssgplabyp9an7mddzkiyjz", 2830 "depends": ["data_table"] 2831 }, 2832 "HPAanalyze": { 2833 "name": "HPAanalyze", 2834 "version": "1.28.0", 2835 "sha256": "1mvn9gxlvsgy8688lrxa1an4mhxr6hhawqqqkxzwgnk68hra9n10", 2836 "depends": ["dplyr", "ggplot2", "gridExtra", "openxlsx", "tibble", "xml2"] 2837 }, 2838 "HTSFilter": { 2839 "name": "HTSFilter", 2840 "version": "1.50.0", 2841 "sha256": "0fk74glws1gf07wz630afjfifvqn5gcacli01l3q5knwhf94x2an", 2842 "depends": ["Biobase", "BiocParallel", "DESeq2", "edgeR"] 2843 }, 2844 "HTqPCR": { 2845 "name": "HTqPCR", 2846 "version": "1.64.0", 2847 "sha256": "1f725965zrmmpf5wxb2l05p8l5d7k9z7b26ac0gxk5m24hnhkmkr", 2848 "depends": ["Biobase", "RColorBrewer", "affy", "gplots", "limma"] 2849 }, 2850 "HVP": { 2851 "name": "HVP", 2852 "version": "1.0.0", 2853 "sha256": "0j2alj0a976lj056lhikapw48kfcdd1xn08d5gclnnwhr0d0nif1", 2854 "depends": ["Matrix"] 2855 }, 2856 "Harman": { 2857 "name": "Harman", 2858 "version": "1.38.0", 2859 "sha256": "028pj0gkky32kz78jfkzxc3q67y7f10sdjiqnf7j5l8y7y38mv7y", 2860 "depends": ["Ckmeans_1d_dp", "Rcpp", "matrixStats"] 2861 }, 2862 "HarmonizR": { 2863 "name": "HarmonizR", 2864 "version": "1.8.0", 2865 "sha256": "0xzniy0z030zbzx90rg6bx4filv3dkzgxihb0lvnvhgrdg67mb8x", 2866 "depends": ["SummarizedExperiment", "doParallel", "foreach", "janitor", "limma", "plyr", "seriation", "sva"] 2867 }, 2868 "Heatplus": { 2869 "name": "Heatplus", 2870 "version": "3.18.0", 2871 "sha256": "1y365hbvvpy785ir2fmzh6wzxvf24g5zh177a5yjhsbl9agmcxyf", 2872 "depends": ["RColorBrewer"] 2873 }, 2874 "HelloRanges": { 2875 "name": "HelloRanges", 2876 "version": "1.36.0", 2877 "sha256": "1az2pvxi9jnbsjk9xva85mbwq95h0wpsp3w9a3cylwwjwmflrg4n", 2878 "depends": ["BSgenome", "BiocGenerics", "BiocIO", "Biostrings", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "docopt", "rtracklayer"] 2879 }, 2880 "Herper": { 2881 "name": "Herper", 2882 "version": "1.20.0", 2883 "sha256": "0ascr9kfk6wxbg6hav0ygkxcb88cqg7fphfa5s43hpiqmkvx6h25", 2884 "depends": ["reticulate", "rjson", "withr"] 2885 }, 2886 "HiCBricks": { 2887 "name": "HiCBricks", 2888 "version": "1.28.0", 2889 "sha256": "03fmkg629vsi38r93lxz1mqf38r051hy8l1djwmr6mcfmfcx5dgw", 2890 "depends": ["BiocParallel", "GenomicRanges", "IRanges", "R6", "RColorBrewer", "R_utils", "S4Vectors", "Seqinfo", "curl", "data_table", "digest", "ggplot2", "jsonlite", "readr", "reshape2", "rhdf5", "scales", "stringr", "tibble", "viridis"] 2891 }, 2892 "HiCDCPlus": { 2893 "name": "HiCDCPlus", 2894 "version": "1.18.0", 2895 "sha256": "1mgdj692ds66c46qzqnhszlww59ab32sg1rq9vqhmf9y27vkcj4i", 2896 "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicInteractions", "GenomicRanges", "IRanges", "InteractionSet", "MASS", "R_utils", "Rcpp", "S4Vectors", "bbmle", "data_table", "dplyr", "pscl", "rlang", "rtracklayer", "tibble", "tidyr"] 2897 }, 2898 "HiCDOC": { 2899 "name": "HiCDOC", 2900 "version": "1.12.0", 2901 "sha256": "1hd259kdg3w3czcr6fczdsabsbqi62ca2y9ym5brykxwh4ak6i5l", 2902 "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "InteractionSet", "Rcpp", "S4Vectors", "Seqinfo", "SummarizedExperiment", "cowplot", "data_table", "ggplot2", "gridExtra", "gtools", "multiHiCcompare", "pbapply"] 2903 }, 2904 "HiCExperiment": { 2905 "name": "HiCExperiment", 2906 "version": "1.10.0", 2907 "sha256": "1gx225p1xx576af9f996gaqqkqpiah8ayfgc9x2p449759jh2x7j", 2908 "depends": ["BiocGenerics", "BiocIO", "BiocParallel", "GenomicRanges", "IRanges", "InteractionSet", "Matrix", "S4Vectors", "Seqinfo", "dplyr", "rhdf5", "strawr", "vroom"] 2909 }, 2910 "HiCParser": { 2911 "name": "HiCParser", 2912 "version": "1.2.0", 2913 "sha256": "17jf2br63q3lfw5ndv0r6pzqx73gc2djfzk5wvl8rbx2x5g8zvis", 2914 "depends": ["BiocGenerics", "GenomicRanges", "InteractionSet", "Rcpp", "S4Vectors", "Seqinfo", "SummarizedExperiment", "data_table", "gtools", "pbapply"] 2915 }, 2916 "HiCPotts": { 2917 "name": "HiCPotts", 2918 "version": "1.0.0", 2919 "sha256": "1bx691rszn4qzisjha4k829a3pf7z268k0vqkbg20xqhqisfcw87", 2920 "depends": ["BSgenome", "BSgenome_Dmelanogaster_UCSC_dm6", "Biostrings", "GenomicRanges", "IRanges", "Rcpp", "RcppArmadillo", "S4Vectors", "rhdf5", "rtracklayer", "strawr"] 2921 }, 2922 "HiCaptuRe": { 2923 "name": "HiCaptuRe", 2924 "version": "1.0.0", 2925 "sha256": "1h0dc584zqqj4h1k7h8d0y6950r15r1mbwdvsmv29kklpagxbd2j", 2926 "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicInteractions", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "UpSetR", "cli", "data_table", "dplyr", "ggVennDiagram", "ggplot2", "ggpubr", "gplots", "igraph", "memoise", "stringr", "tibble", "tidyr"] 2927 }, 2928 "HiCcompare": { 2929 "name": "HiCcompare", 2930 "version": "1.32.0", 2931 "sha256": "1q8w2m588pvsnv907mpz2n9q64230m0ijy3wnvzi6iy4wgkcwh6g", 2932 "depends": ["BiocParallel", "GenomicRanges", "IRanges", "InteractionSet", "KernSmooth", "S4Vectors", "data_table", "dplyr", "ggplot2", "gridExtra", "gtools", "mgcv", "pheatmap", "rhdf5"] 2933 }, 2934 "HiContacts": { 2935 "name": "HiContacts", 2936 "version": "1.12.0", 2937 "sha256": "1qanyvd68z3v6x6570hh54ppqmx3k9v8r2z0ykc5a1wa6xi9cwp1", 2938 "depends": ["BiocGenerics", "BiocIO", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "HiCExperiment", "IRanges", "InteractionSet", "Matrix", "RSpectra", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "ggrastr", "readr", "scales", "stringr", "tibble", "tidyr"] 2939 }, 2940 "HiLDA": { 2941 "name": "HiLDA", 2942 "version": "1.24.0", 2943 "sha256": "15jh2brpk0kz15hra2h3fw5fygarxi5dgd6d1cmrbx4pxizg9lbc", 2944 "depends": ["BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "Biostrings", "GenomicFeatures", "GenomicRanges", "R2jags", "Rcpp", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "XVector", "abind", "cowplot", "forcats", "ggplot2", "stringr", "tidyr"] 2945 }, 2946 "HiTC": { 2947 "name": "HiTC", 2948 "version": "1.54.0", 2949 "sha256": "0jnqp4n0yzrvfbrs29hz8spyafqcz4c1r7iym089m260l5l93y3n", 2950 "depends": ["Biostrings", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "Seqinfo", "rtracklayer"] 2951 }, 2952 "HicAggR": { 2953 "name": "HicAggR", 2954 "version": "1.6.0", 2955 "sha256": "1dqbbd049slzzlypfsjswaqvxrq724smcm2d4sbjq82ngrlgi9wx", 2956 "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "InteractionSet", "Matrix", "S4Vectors", "Seqinfo", "checkmate", "data_table", "dplyr", "ggplot2", "gridExtra", "purrr", "reshape", "rhdf5", "rlang", "rtracklayer", "strawr", "stringr", "tibble", "tidyr", "withr"] 2957 }, 2958 "HilbertCurve": { 2959 "name": "HilbertCurve", 2960 "version": "2.4.0", 2961 "sha256": "0c9j2isy67012hyzfy8m30l900r9g4cfkcir1jvkcl3p8ndk74pj", 2962 "depends": ["GenomicRanges", "IRanges", "Rcpp", "circlize", "png", "polylabelr"] 2963 }, 2964 "HilbertVis": { 2965 "name": "HilbertVis", 2966 "version": "1.68.0", 2967 "sha256": "0x7bvirqibj0bykhv4f1qji8mbrsm288l9d901jjbvrwd0nfmh04", 2968 "depends": ["lattice"] 2969 }, 2970 "HilbertVisGUI": { 2971 "name": "HilbertVisGUI", 2972 "version": "1.68.0", 2973 "sha256": "0c5fvhplpqmap0nsc04mlmybb5d092y655lyj771b1hpp40yd0dh", 2974 "depends": ["HilbertVis"] 2975 }, 2976 "HoloFoodR": { 2977 "name": "HoloFoodR", 2978 "version": "1.4.0", 2979 "sha256": "1y7q3kldwdmj57jd6wy24ss0fw254sy6794lllhd98r2crp7qqv9", 2980 "depends": ["MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "dplyr", "httr2", "jsonlite", "stringi"] 2981 }, 2982 "HuBMAPR": { 2983 "name": "HuBMAPR", 2984 "version": "1.4.0", 2985 "sha256": "0frk061x9f1h5ypvnkqm1j940aqzysla6x095wll9f17vjl29zpx", 2986 "depends": ["dplyr", "httr2", "purrr", "rjsoncons", "rlang", "stringr", "tibble", "tidyr", "whisker"] 2987 }, 2988 "HubPub": { 2989 "name": "HubPub", 2990 "version": "1.18.0", 2991 "sha256": "0vfjwncf9b9swngm360xfy7mblmw6bymqgs77v9qc3qd2wswydg8", 2992 "depends": ["BiocManager", "available", "aws_s3", "biocthis", "dplyr", "fs", "usethis"] 2993 }, 2994 "HybridExpress": { 2995 "name": "HybridExpress", 2996 "version": "1.6.0", 2997 "sha256": "1awlw7q3c60qs507dy3dcvip3si2ds4qjpl9bc4fzy7wjnc2nfym", 2998 "depends": ["BiocParallel", "ComplexHeatmap", "DESeq2", "RColorBrewer", "SummarizedExperiment", "ggplot2", "patchwork", "rlang"] 2999 }, 3000 "HybridMTest": { 3001 "name": "HybridMTest", 3002 "version": "1.54.0", 3003 "sha256": "0cyzag5b1c5i6dpykpgl08dlgsdqz3pwfz9yq6ycy0yv9i78hqi5", 3004 "depends": ["Biobase", "MASS", "fdrtool", "survival"] 3005 }, 3006 "IFAA": { 3007 "name": "IFAA", 3008 "version": "1.12.0", 3009 "sha256": "1pyq3k6v7f6a1993mnp1g45l6yp2yarzazkvvfq42qccgqx37r60", 3010 "depends": ["DescTools", "HDCI", "Matrix", "MatrixExtra", "S4Vectors", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "glmnet", "mathjaxr", "parallelly", "stringr"] 3011 }, 3012 "IHW": { 3013 "name": "IHW", 3014 "version": "1.38.0", 3015 "sha256": "02ni484hfw9r76shdq1hchlr11i6h6c5p620ybqfw6vk0cr6nb6g", 3016 "depends": ["BiocGenerics", "fdrtool", "lpsymphony", "slam"] 3017 }, 3018 "ILoReg": { 3019 "name": "ILoReg", 3020 "version": "1.20.0", 3021 "sha256": "1bik7wni596n7vhxzx81xp41sadqs8ynmm6d4mxyya82qyymvzj9", 3022 "depends": ["DescTools", "LiblineaR", "Matrix", "RSpectra", "Rtsne", "S4Vectors", "SingleCellExperiment", "SparseM", "SummarizedExperiment", "aricode", "cluster", "cowplot", "dendextend", "doRNG", "doSNOW", "dplyr", "fastcluster", "foreach", "ggplot2", "parallelDist", "pheatmap", "plyr", "reshape2", "scales", "umap"] 3023 }, 3024 "IMMAN": { 3025 "name": "IMMAN", 3026 "version": "1.30.0", 3027 "sha256": "1fwvc3x8cir66dp414f0x0d1i5c15nyi8zvb108zycl7m411hk89", 3028 "depends": ["STRINGdb", "igraph", "pwalign", "seqinr"] 3029 }, 3030 "IMPCdata": { 3031 "name": "IMPCdata", 3032 "version": "1.46.0", 3033 "sha256": "0k9wn6daydbpsxlflc395iimghcq20ik42sf8fsvm6kvzkmq388p", 3034 "depends": ["rjson"] 3035 }, 3036 "INDEED": { 3037 "name": "INDEED", 3038 "version": "2.24.0", 3039 "sha256": "0s5crvplgalw394x8fknpicnxipg09051ib0jbbwix1xb0r68car", 3040 "depends": ["devtools", "glasso", "igraph", "visNetwork"] 3041 }, 3042 "INPower": { 3043 "name": "INPower", 3044 "version": "1.46.0", 3045 "sha256": "15p46b8wgwmv289kg5hw97inigq49jyb90y9klg6fqv8rwlghpxm", 3046 "depends": ["mvtnorm"] 3047 }, 3048 "INSPEcT": { 3049 "name": "INSPEcT", 3050 "version": "1.40.0", 3051 "sha256": "1wfnwrgnpsrvavqdbvj57llgjf0j7yljpyhlbxbp0gbmxs9i1bnf", 3052 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "KernSmooth", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TxDb_Mmusculus_UCSC_mm9_knownGene", "deSolve", "pROC", "plgem", "readxl", "rootSolve", "rtracklayer", "shiny"] 3053 }, 3054 "INTACT": { 3055 "name": "INTACT", 3056 "version": "1.10.0", 3057 "sha256": "1hlwmy4fmvrw9v3wr02jjrlj9xmdkvsd1dq4h13rfbdcfkbisxla", 3058 "depends": ["SQUAREM", "bdsmatrix", "ggplot2", "numDeriv", "tidyr"] 3059 }, 3060 "IONiseR": { 3061 "name": "IONiseR", 3062 "version": "2.34.0", 3063 "sha256": "1zz8sfjbimdmjq3dv6jpsvw8yf8yig8656rdmp30xh4407ks4br6", 3064 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "ShortRead", "XVector", "bit64", "dplyr", "ggplot2", "magrittr", "rhdf5", "stringr", "tibble", "tidyr"] 3065 }, 3066 "IPO": { 3067 "name": "IPO", 3068 "version": "1.36.0", 3069 "sha256": "147554d7jg47hm1jawa4wg9fzv7z00kyxw8babr6r6q0qdz78il7", 3070 "depends": ["BiocParallel", "CAMERA", "rsm", "xcms"] 3071 }, 3072 "IRanges": { 3073 "name": "IRanges", 3074 "version": "2.44.0", 3075 "sha256": "0hjhc244p67gnlg2f1x71p6rypmkggn1sqp8r8psw1aq9355aki4", 3076 "depends": ["BiocGenerics", "S4Vectors"] 3077 }, 3078 "ISAnalytics": { 3079 "name": "ISAnalytics", 3080 "version": "1.20.0", 3081 "sha256": "1b6q0cx3nvklp5458gs8qb33d0fs362y9sp90snjpajs52n07ilw", 3082 "depends": ["DT", "bslib", "data_table", "datamods", "dplyr", "forcats", "fs", "ggplot2", "ggrepel", "glue", "lifecycle", "lubridate", "purrr", "readr", "readxl", "rlang", "shiny", "shinyWidgets", "stringr", "tibble", "tidyr", "vegan"] 3083 }, 3084 "ISLET": { 3085 "name": "ISLET", 3086 "version": "1.12.0", 3087 "sha256": "0snwx7q5069afg31y4k20d6qy4ygdp6bz5xprj3wxkm25vmc8pkk", 3088 "depends": ["BiocGenerics", "BiocParallel", "Matrix", "SummarizedExperiment", "abind", "lme4", "nnls", "purrr"] 3089 }, 3090 "ISoLDE": { 3091 "name": "ISoLDE", 3092 "version": "1.38.0", 3093 "sha256": "0mfijii5fa9f6n94xrwjlp0wj3d21d777rh9gbrx42smp0zqa165", 3094 "depends": [] 3095 }, 3096 "ITALICS": { 3097 "name": "ITALICS", 3098 "version": "2.70.0", 3099 "sha256": "1rvj1wnlr4534fwxm9qngn1nlmm2s3lrq15h4fh2xk0rwvshdksz", 3100 "depends": ["DBI", "GLAD", "ITALICSData", "affxparser", "oligo", "oligoClasses", "pd_mapping50k_xba240"] 3101 }, 3102 "IVAS": { 3103 "name": "IVAS", 3104 "version": "2.30.0", 3105 "sha256": "0wzcrcq9rdi93fry36q17lm80nsrqwccqbk57sapjb2rfdbymc7c", 3106 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "Seqinfo", "doParallel", "foreach", "ggfortify", "ggplot2", "lme4"] 3107 }, 3108 "IWTomics": { 3109 "name": "IWTomics", 3110 "version": "1.33.0", 3111 "sha256": "048vwzidmpzbbl3ymqc6in7xlhj2gcq35gmm88kl2knfc04i3qg5", 3112 "depends": ["GenomicRanges", "IRanges", "KernSmooth", "S4Vectors", "fda", "gtable"] 3113 }, 3114 "Ibex": { 3115 "name": "Ibex", 3116 "version": "1.0.0", 3117 "sha256": "1x97y9ilnpq3qj2ynfblgr0xjbrq4ayimgjsbs1wbg2p09l14b7b", 3118 "depends": ["Matrix", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "basilisk", "immApex", "reticulate", "rlang", "scRepertoire", "tensorflow"] 3119 }, 3120 "Icens": { 3121 "name": "Icens", 3122 "version": "1.82.0", 3123 "sha256": "1w7bivsbp6l6nwvgqbx9rgw9v21mrs0lwvxwydmqgfk8z346f2ij", 3124 "depends": ["survival"] 3125 }, 3126 "IdeoViz": { 3127 "name": "IdeoViz", 3128 "version": "1.46.0", 3129 "sha256": "13f53pp0wdmlsapj03yg7kqf5n2qpbxr7iz7p7wgv1ljv6jri0ds", 3130 "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "rtracklayer"] 3131 }, 3132 "IgGeneUsage": { 3133 "name": "IgGeneUsage", 3134 "version": "1.24.0", 3135 "sha256": "1fdmmqs4jsh482c7q5m49p39ln8aw6v19n87sdm6l93d4rlzmj5q", 3136 "depends": ["BH", "Rcpp", "RcppEigen", "RcppParallel", "StanHeaders", "SummarizedExperiment", "reshape2", "rstan", "rstantools", "tidyr"] 3137 }, 3138 "InPAS": { 3139 "name": "InPAS", 3140 "version": "2.18.0", 3141 "sha256": "1lw65cizag8ng79ycr0rfvbgg7913dk4297wr0mhzbli5f9jh788", 3142 "depends": ["AnnotationDbi", "BSgenome", "Biobase", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "Seqinfo", "batchtools", "cleanUpdTSeq", "depmixS4", "dplyr", "flock", "future", "future_apply", "ggplot2", "limma", "magrittr", "parallelly", "plyranges", "preprocessCore", "readr", "reshape2"] 3143 }, 3144 "InTAD": { 3145 "name": "InTAD", 3146 "version": "1.30.0", 3147 "sha256": "15g67ivr7f765274lyrjjddsm0j8laj56cv1jai054cp2wms8cxk", 3148 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "ggplot2", "ggpubr", "mclust", "qvalue", "rtracklayer"] 3149 }, 3150 "Informeasure": { 3151 "name": "Informeasure", 3152 "version": "1.20.0", 3153 "sha256": "1l70grlg9cb781hlphbdb3g2zhni566lbfy8nhp493lshx6pjdpx", 3154 "depends": ["entropy"] 3155 }, 3156 "IntEREst": { 3157 "name": "IntEREst", 3158 "version": "1.34.0", 3159 "sha256": "0nrzwa74nsyrcyjcalbpr05xb8njadwmh5xwmhiv5bcg8q4qbhyw", 3160 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "DBI", "DESeq2", "DEXSeq", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "IRanges", "RMariaDB", "Rsamtools", "S4Vectors", "SummarizedExperiment", "edgeR", "seqLogo", "seqinr", "txdbmaker"] 3161 }, 3162 "InterCellar": { 3163 "name": "InterCellar", 3164 "version": "2.16.0", 3165 "sha256": "0h7h5h11xhxq9879y4h61lk8ymwkz7nl5236blqy58mardh31ngl", 3166 "depends": ["ComplexHeatmap", "DT", "biomaRt", "circlize", "colorspace", "colourpicker", "config", "data_table", "dendextend", "dplyr", "factoextra", "fmsb", "fs", "ggplot2", "golem", "htmltools", "htmlwidgets", "igraph", "plotly", "plyr", "readxl", "rlang", "scales", "shiny", "shinyFeedback", "shinyFiles", "shinyalert", "shinycssloaders", "shinydashboard", "signal", "tibble", "tidyr", "umap", "visNetwork", "wordcloud2"] 3167 }, 3168 "InteractionSet": { 3169 "name": "InteractionSet", 3170 "version": "1.38.0", 3171 "sha256": "0n2gncrb9ghvg4nx1dykyhq17vxzhjzj7va9r6iwpcmgyizpph5a", 3172 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "S4Vectors", "Seqinfo", "SummarizedExperiment"] 3173 }, 3174 "InteractiveComplexHeatmap": { 3175 "name": "InteractiveComplexHeatmap", 3176 "version": "1.18.0", 3177 "sha256": "1fqkrf3mwfxd1sf813vxx23nj1zh4la43byxiglc4adf6s8mh67p", 3178 "depends": ["ComplexHeatmap", "GetoptLong", "IRanges", "RColorBrewer", "S4Vectors", "clisymbols", "digest", "fontawesome", "htmltools", "jsonlite", "kableExtra", "shiny", "svglite"] 3179 }, 3180 "IntramiRExploreR": { 3181 "name": "IntramiRExploreR", 3182 "version": "1.32.0", 3183 "sha256": "0yj9x04zbgh5k6d1clmmdmmj6jc9fa4492q54bjzj5kvgxrlfp55", 3184 "depends": ["FGNet", "igraph", "knitr"] 3185 }, 3186 "IsoBayes": { 3187 "name": "IsoBayes", 3188 "version": "1.8.0", 3189 "sha256": "0xgy7gnn6gngayas864wqs86ih0jkgirz9bvaxj3jmnd0rv84maz", 3190 "depends": ["HDInterval", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "data_table", "doParallel", "doRNG", "foreach", "ggplot2", "glue", "iterators"] 3191 }, 3192 "IsoCorrectoR": { 3193 "name": "IsoCorrectoR", 3194 "version": "1.28.0", 3195 "sha256": "1h76d3pmx7fzprvkb2rs9zcdss49p0zpkq5rj4ci4rv7pzf8dp53", 3196 "depends": ["WriteXLS", "dplyr", "magrittr", "pracma", "quadprog", "readr", "readxl", "stringr", "tibble"] 3197 }, 3198 "IsoCorrectoRGUI": { 3199 "name": "IsoCorrectoRGUI", 3200 "version": "1.26.0", 3201 "sha256": "0m79392xz8snhmc3mngpzv80dzl76j4mhpg9m09jpdj5y168mvdy", 3202 "depends": ["IsoCorrectoR", "readxl", "tcltk2"] 3203 }, 3204 "IsoformSwitchAnalyzeR": { 3205 "name": "IsoformSwitchAnalyzeR", 3206 "version": "2.10.0", 3207 "sha256": "03xc279lhysn4lilmgi0fbx6a57xx0d31h0nyibw79qh3m14lisl", 3208 "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DBI", "DEXSeq", "GenomicRanges", "IRanges", "RColorBrewer", "RCurl", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VennDiagram", "XVector", "dplyr", "edgeR", "futile_logger", "ggplot2", "gridExtra", "limma", "magrittr", "pfamAnalyzeR", "plyr", "pwalign", "readr", "reshape2", "rtracklayer", "satuRn", "stringr", "sva", "tibble", "tidyr", "tximeta", "tximport"] 3209 }, 3210 "KBoost": { 3211 "name": "KBoost", 3212 "version": "1.18.0", 3213 "sha256": "0wiz3s2zfypvgqxkg4qsyvcnh08cnkrsnmag97b932qx1fkxj0w7", 3214 "depends": [] 3215 }, 3216 "KCsmart": { 3217 "name": "KCsmart", 3218 "version": "2.68.0", 3219 "sha256": "1ki1khbs5gv2y4iysmf19dhxinlmrhi6xq0h1dj18avv1ng044xh", 3220 "depends": ["BiocGenerics", "KernSmooth", "multtest", "siggenes"] 3221 }, 3222 "KEGGREST": { 3223 "name": "KEGGREST", 3224 "version": "1.50.0", 3225 "sha256": "09awamalar3w55yqcknkhvsj7zf3jwh8m5dbwc22pl5lij1w3mc5", 3226 "depends": ["Biostrings", "httr", "png"] 3227 }, 3228 "KEGGgraph": { 3229 "name": "KEGGgraph", 3230 "version": "1.70.0", 3231 "sha256": "1d97w3q3rbnrcv0bqgns61sxxy2yynd6ibd14g4mjlfapyfa005z", 3232 "depends": ["RCurl", "Rgraphviz", "XML", "graph"] 3233 }, 3234 "KEGGlincs": { 3235 "name": "KEGGlincs", 3236 "version": "1.36.0", 3237 "sha256": "01h49khx6fc654i55mjxpv3fy80rrqgmmczhvx18gjinrmckxzka", 3238 "depends": ["AnnotationDbi", "KEGGREST", "KEGGgraph", "KOdata", "RJSONIO", "XML", "gtools", "hgu133a_db", "httr", "igraph", "org_Hs_eg_db", "plyr"] 3239 }, 3240 "KinSwingR": { 3241 "name": "KinSwingR", 3242 "version": "1.28.0", 3243 "sha256": "1v8ba5jbgc5q67xgj4ikkp8il0z444hywl47i3sshv7r6m86f9jv", 3244 "depends": ["BiocParallel", "data_table", "sqldf"] 3245 }, 3246 "KnowSeq": { 3247 "name": "KnowSeq", 3248 "version": "1.24.0", 3249 "sha256": "1955z0dhb0dr4lpcyiwk4l6jg7l31bkh2ff0w1ypinrkkg7khrqd", 3250 "depends": ["Hmisc", "R_utils", "XML", "caret", "cqn", "e1071", "edgeR", "ggplot2", "gridExtra", "httr", "jsonlite", "kernlab", "limma", "praznik", "randomForest", "reshape2", "rlist", "rmarkdown", "stringr", "sva"] 3251 }, 3252 "LACE": { 3253 "name": "LACE", 3254 "version": "2.14.0", 3255 "sha256": "09ibw1gj6hmswl5bs10h0r9n7pxqfffyfq2bcvvvn2jfsvdhhlzl", 3256 "depends": ["DT", "Matrix", "RColorBrewer", "Rfast", "SummarizedExperiment", "biomaRt", "bsplus", "callr", "configr", "curl", "data_table", "data_tree", "doParallel", "dplyr", "forcats", "foreach", "fs", "ggplot2", "htmltools", "htmlwidgets", "igraph", "jsonlite", "logr", "purrr", "readr", "shiny", "shinyBS", "shinyFiles", "shinydashboard", "shinyjs", "shinythemes", "shinyvalidate", "sortable", "stringi", "stringr", "svglite", "tidyr"] 3257 }, 3258 "LBE": { 3259 "name": "LBE", 3260 "version": "1.78.0", 3261 "sha256": "0rbd4a3cpd19qb2f079rh28pjqanxgk8by4krdd22lj6gi97h1pg", 3262 "depends": [] 3263 }, 3264 "LEA": { 3265 "name": "LEA", 3266 "version": "3.22.0", 3267 "sha256": "14qpp18m3m9mwg2w4b7bm6218vs5ik2zk6m1wln4jd8rcn51dsxm", 3268 "depends": [] 3269 }, 3270 "LOBSTAHS": { 3271 "name": "LOBSTAHS", 3272 "version": "1.36.0", 3273 "sha256": "0bf2v7cckv34b3biqknwlpm8d9fkzbm5fkz1xvg528xwjk884m2f", 3274 "depends": ["CAMERA", "xcms"] 3275 }, 3276 "LOLA": { 3277 "name": "LOLA", 3278 "version": "1.39.1", 3279 "sha256": "1r1c7am8qdwll7vl9lz15hx9c0srcq9y9dwl46r4wzdlfq9nwic0", 3280 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "data_table", "reshape2"] 3281 }, 3282 "LPE": { 3283 "name": "LPE", 3284 "version": "1.84.0", 3285 "sha256": "000yaas7w28hzj61swwcy9ak6826syrhqriqqr0q0fdpgn881nhi", 3286 "depends": [] 3287 }, 3288 "LRBaseDbi": { 3289 "name": "LRBaseDbi", 3290 "version": "2.20.0", 3291 "sha256": "1j9q9h3x9chxjfbw12rf64b6m4fax1rzsx17rsxspxr59ka82q56", 3292 "depends": ["AnnotationDbi", "Biobase", "DBI", "RSQLite"] 3293 }, 3294 "LRcell": { 3295 "name": "LRcell", 3296 "version": "1.18.0", 3297 "sha256": "0r5ck7clad67prlraj85nv90glmhwazvr8qr8qnl1nr3jby67613", 3298 "depends": ["AnnotationHub", "BiocParallel", "ExperimentHub", "dplyr", "ggplot2", "ggrepel", "magrittr"] 3299 }, 3300 "LedPred": { 3301 "name": "LedPred", 3302 "version": "1.44.0", 3303 "sha256": "0mvac9bx7fqa7kwbm9w7snrnc19bvg01di6cx1r1hi3qg3gwybs4", 3304 "depends": ["RCurl", "ROCR", "akima", "e1071", "ggplot2", "irr", "jsonlite", "plot3D", "plyr", "testthat"] 3305 }, 3306 "Lheuristic": { 3307 "name": "Lheuristic", 3308 "version": "1.2.0", 3309 "sha256": "16aq8vq6bpvbr1c8f11nky416ajk5rr31r316mncvpl45b0azq9m", 3310 "depends": ["Hmisc", "MultiAssayExperiment", "energy", "ggplot2", "ggpubr"] 3311 }, 3312 "LimROTS": { 3313 "name": "LimROTS", 3314 "version": "1.2.0", 3315 "sha256": "1yb7mzz0kgpspmfkgj93aa341zd58rcvpd46iq4mrdy84g85ijym", 3316 "depends": ["BiocParallel", "S4Vectors", "SummarizedExperiment", "dplyr", "limma", "qvalue", "stringr"] 3317 }, 3318 "LinkHD": { 3319 "name": "LinkHD", 3320 "version": "1.24.0", 3321 "sha256": "11v2sr9ascq2h1595r9qhal2p9frqin3a9frck90zch23hv59qlw", 3322 "depends": ["MultiAssayExperiment", "cluster", "data_table", "emmeans", "ggplot2", "ggpubr", "gridExtra", "reshape2", "rio", "scales", "vegan"] 3323 }, 3324 "Linnorm": { 3325 "name": "Linnorm", 3326 "version": "2.34.0", 3327 "sha256": "0zh6pwfglgxhjp71ac0vqygazjsmg5pnwfh32i2nc6qrfp22f86d", 3328 "depends": ["MASS", "Rcpp", "RcppArmadillo", "Rtsne", "amap", "apcluster", "ellipse", "fastcluster", "fpc", "ggdendro", "ggplot2", "gmodels", "igraph", "limma", "mclust", "statmod", "vegan", "zoo"] 3329 }, 3330 "LipidTrend": { 3331 "name": "LipidTrend", 3332 "version": "1.0.0", 3333 "sha256": "1d2kw6n0r8v2zhwnxvl14a4ri4z7418nqbbl5l2krfhd3p48v0bf", 3334 "depends": ["MKmisc", "SummarizedExperiment", "dplyr", "ggnewscale", "ggplot2", "magrittr", "matrixTests", "rlang"] 3335 }, 3336 "LiquidAssociation": { 3337 "name": "LiquidAssociation", 3338 "version": "1.64.0", 3339 "sha256": "1wcdmhnphgb1yrvgahxk6bx9xigcrxjz2ivs1i4qfwxa8gwp9g84", 3340 "depends": ["Biobase", "geepack", "org_Sc_sgd_db", "yeastCC"] 3341 }, 3342 "LoomExperiment": { 3343 "name": "LoomExperiment", 3344 "version": "1.28.0", 3345 "sha256": "0n0bkjl93l58glbk4llzy39b9s9yc5nq28fnr77dsl5piz4vvvqp", 3346 "depends": ["BiocIO", "DelayedArray", "GenomicRanges", "HDF5Array", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "rhdf5", "stringr"] 3347 }, 3348 "LymphoSeq": { 3349 "name": "LymphoSeq", 3350 "version": "1.38.0", 3351 "sha256": "1n4dx54x5dgclc14vfcd91q3yy2dsz5jb5z4l5m2jy1csz4lr05d", 3352 "depends": ["Biostrings", "LymphoSeqDB", "RColorBrewer", "UpSetR", "VennDiagram", "circlize", "data_table", "dplyr", "ggplot2", "ggtree", "ineq", "msa", "phangorn", "plyr", "reshape", "stringdist"] 3353 }, 3354 "M3C": { 3355 "name": "M3C", 3356 "version": "1.32.0", 3357 "sha256": "0g5lq89hh9q6lb09zpfh0z0zp5nq6h585mv1x68w8zd3y5ws5r5z", 3358 "depends": ["Matrix", "Rtsne", "cluster", "corpcor", "doParallel", "doSNOW", "foreach", "ggplot2", "matrixcalc", "umap"] 3359 }, 3360 "M3Drop": { 3361 "name": "M3Drop", 3362 "version": "1.36.0", 3363 "sha256": "0w32rpc5v20iyix3xdcn9fvcwp1wk9p5wnilsxl0kwwi0n462vgb", 3364 "depends": ["Hmisc", "Matrix", "RColorBrewer", "bbmle", "gplots", "irlba", "matrixStats", "numDeriv", "reldist", "scater", "statmod"] 3365 }, 3366 "MACSQuantifyR": { 3367 "name": "MACSQuantifyR", 3368 "version": "1.24.0", 3369 "sha256": "1jld2v0r3h7y6p1fx0wp84f34cv26cayhvhsq8any4wkglhp4ksa", 3370 "depends": ["ggplot2", "ggrepel", "gridExtra", "lattice", "latticeExtra", "png", "prettydoc", "readxl", "rmarkdown", "rvest", "xml2"] 3371 }, 3372 "MACSr": { 3373 "name": "MACSr", 3374 "version": "1.18.0", 3375 "sha256": "1i64jxwqi3f4hkbhyzsybpxpiaz3lv936cxahms88i3mqq9yxrrm", 3376 "depends": ["AnnotationHub", "ExperimentHub", "S4Vectors", "basilisk", "reticulate"] 3377 }, 3378 "MAGAR": { 3379 "name": "MAGAR", 3380 "version": "1.18.0", 3381 "sha256": "0xw3ikfv3zmzjw2agjajr715ala029lpb4g1y8qhq83l1ma06hxr", 3382 "depends": ["HDF5Array", "RnBeads", "RnBeads_hg19", "RnBeads_hg38", "UpSetR", "argparse", "bigstatsr", "crlmm", "data_table", "doParallel", "ff", "igraph", "impute", "jsonlite", "plyr", "reshape2", "rjson", "snpStats"] 3383 }, 3384 "MAI": { 3385 "name": "MAI", 3386 "version": "1.16.0", 3387 "sha256": "14zk3x9kja7y5b8lljia2ndj4iin01j8vgq9fw3plrnh0jbrawsv", 3388 "depends": ["S4Vectors", "SummarizedExperiment", "caret", "doParallel", "e1071", "foreach", "future", "future_apply", "missForest", "pcaMethods", "tidyverse"] 3389 }, 3390 "MAIT": { 3391 "name": "MAIT", 3392 "version": "1.44.0", 3393 "sha256": "1x4fd01jbzb6h8gwx4himwizyflzwa43cn7w1aql70bl26184hda", 3394 "depends": ["CAMERA", "MASS", "Rcpp", "agricolae", "caret", "class", "e1071", "gplots", "pls", "plsgenomics", "xcms"] 3395 }, 3396 "MANOR": { 3397 "name": "MANOR", 3398 "version": "1.82.0", 3399 "sha256": "0bgv10b2639mcsvayxg7fv7jijvaz8nd0s0gp7lx62ddq1npw367", 3400 "depends": ["GLAD"] 3401 }, 3402 "MAPFX": { 3403 "name": "MAPFX", 3404 "version": "1.6.0", 3405 "sha256": "1fwdy5jv44bx0sbhqgi9mm1h144d7wak6j5q97np4pir2rg4b3qj", 3406 "depends": ["Biobase", "ComplexHeatmap", "RColorBrewer", "Rfast", "circlize", "cowplot", "e1071", "flowCore", "ggplot2", "glmnetUtils", "gtools", "iCellR", "igraph", "pbapply", "reshape2", "stringr", "uwot", "xgboost"] 3407 }, 3408 "MAST": { 3409 "name": "MAST", 3410 "version": "1.36.0", 3411 "sha256": "1q0r9288k7jz3brsprmdc3a2h6x2nji4x7pdbd5vsrz32xrjcydw", 3412 "depends": ["Biobase", "BiocGenerics", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "abind", "data_table", "ggplot2", "plyr", "progress", "reshape2", "stringr"] 3413 }, 3414 "MBASED": { 3415 "name": "MBASED", 3416 "version": "1.44.0", 3417 "sha256": "07kkwigxg2d0c3vz3zf4vqim4b2gsv5fsk7z8pbcjjpbbf5dr392", 3418 "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "RUnit", "SummarizedExperiment"] 3419 }, 3420 "MBAmethyl": { 3421 "name": "MBAmethyl", 3422 "version": "1.44.0", 3423 "sha256": "0fcdp6jbk6bjha9jm6lp6g99yyalsdhlzwdr5jalfhddbag5bsr9", 3424 "depends": [] 3425 }, 3426 "MBCB": { 3427 "name": "MBCB", 3428 "version": "1.64.0", 3429 "sha256": "1nkjkp5gmyjsa07av154hrwb6slykzl2ls9f9y6417qhni5xznhv", 3430 "depends": ["preprocessCore", "tcltk2"] 3431 }, 3432 "MBECS": { 3433 "name": "MBECS", 3434 "version": "1.14.0", 3435 "sha256": "1l0qgsf2jw9mjrahw79axa7pmwdrhywfzmcjdli5533i5lg4df1v", 3436 "depends": ["Matrix", "cluster", "dplyr", "ggplot2", "gridExtra", "limma", "lme4", "lmerTest", "magrittr", "pheatmap", "phyloseq", "rmarkdown", "ruv", "sva", "tibble", "tidyr", "vegan"] 3437 }, 3438 "MBQN": { 3439 "name": "MBQN", 3440 "version": "2.22.0", 3441 "sha256": "0i1qdssiicjwxll12avyshmd6sy3rjxilxgihx9xv70wpkl8x18i", 3442 "depends": ["BiocFileCache", "PairedData", "RCurl", "SummarizedExperiment", "ggplot2", "limma", "preprocessCore", "rappdirs", "rmarkdown", "xml2"] 3443 }, 3444 "MBttest": { 3445 "name": "MBttest", 3446 "version": "1.38.0", 3447 "sha256": "0531zxc51fp1cc9jb5c8vlvki4f5vqlgqnjag9zx5n62c2ik37fq", 3448 "depends": ["gplots", "gtools"] 3449 }, 3450 "MCbiclust": { 3451 "name": "MCbiclust", 3452 "version": "1.34.0", 3453 "sha256": "15sr0m29nw0ypiqj4hr1axxkghyn5iclr3p9s763ixkiiqakbppy", 3454 "depends": ["AnnotationDbi", "BiocParallel", "GGally", "GO_db", "WGCNA", "cluster", "ggplot2", "org_Hs_eg_db", "scales"] 3455 }, 3456 "MDTS": { 3457 "name": "MDTS", 3458 "version": "1.30.0", 3459 "sha256": "1j2k9hvl9h16c4vc59q4v1n9xrqiilk0rkxvj5pgy5vihh90nlnj", 3460 "depends": ["Biostrings", "DNAcopy", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "stringr"] 3461 }, 3462 "MEAL": { 3463 "name": "MEAL", 3464 "version": "1.40.0", 3465 "sha256": "0vc1zz5x4d004k0hdglzv0cjz1y8w6n8568ns801x5dyhj651ywf", 3466 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "MultiDataSet", "S4Vectors", "SmartSVA", "SummarizedExperiment", "ggplot2", "isva", "limma", "matrixStats", "minfi", "missMethyl", "permute", "vegan"] 3467 }, 3468 "MEAT": { 3469 "name": "MEAT", 3470 "version": "1.22.0", 3471 "sha256": "1l8v3i99wkvan1fi9d2g62d1pq5j2kvk13bf9hp4wdqqfb3rg62n", 3472 "depends": ["RPMM", "SummarizedExperiment", "dplyr", "dynamicTreeCut", "glmnet", "impute", "minfi", "stringr", "tibble", "wateRmelon"] 3473 }, 3474 "MEB": { 3475 "name": "MEB", 3476 "version": "1.24.0", 3477 "sha256": "049bbl5hpy3c49vp7dssfg75rvbhbpg6zccnjx4dsr68nxmqqxmp", 3478 "depends": ["SingleCellExperiment", "SummarizedExperiment", "e1071", "edgeR", "scater", "wrswoR"] 3479 }, 3480 "MEDIPS": { 3481 "name": "MEDIPS", 3482 "version": "1.62.0", 3483 "sha256": "1cwisrklpzna284vgnllpm5f950w3kq45rngjqi4mdngpj5mq1lf", 3484 "depends": ["BSgenome", "Biostrings", "DNAcopy", "GenomicRanges", "IRanges", "Rsamtools", "biomaRt", "edgeR", "gtools", "preprocessCore", "rtracklayer"] 3485 }, 3486 "MEDME": { 3487 "name": "MEDME", 3488 "version": "1.70.0", 3489 "sha256": "13lngv3q33kirygkw7spxyn6bff58fglxzkifficxz2z9d3n2q9y", 3490 "depends": ["Biostrings", "MASS", "drc"] 3491 }, 3492 "MEIGOR": { 3493 "name": "MEIGOR", 3494 "version": "1.44.0", 3495 "sha256": "1ybv8q9q9k84vnhy57zxisy1r8ya0555c77mcjrziqlzvw6zf1fr", 3496 "depends": ["CNORode", "Rsolnp", "deSolve", "snowfall"] 3497 }, 3498 "MGFM": { 3499 "name": "MGFM", 3500 "version": "1.44.0", 3501 "sha256": "0bjnjpdba75wlsw9n17vywa09g5d0n741wlxmn2f61hipn6ajzgr", 3502 "depends": ["AnnotationDbi", "annotate"] 3503 }, 3504 "MGnifyR": { 3505 "name": "MGnifyR", 3506 "version": "1.6.0", 3507 "sha256": "0p60i8xlfpz742j3ypz9vbcmn7ndkxaqfixcfvxwkj3v32yfij91", 3508 "depends": ["BiocGenerics", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "dplyr", "httr", "mia", "plyr", "reshape2", "tidyjson", "urltools"] 3509 }, 3510 "MICSQTL": { 3511 "name": "MICSQTL", 3512 "version": "1.8.0", 3513 "sha256": "1w8pffapjy26vmwvhh58890nj8pjb2105hdf4gmfvh4zn5rvr41c", 3514 "depends": ["BiocParallel", "S4Vectors", "SummarizedExperiment", "TCA", "TOAST", "dirmult", "ggplot2", "ggpubr", "ggridges", "glue", "magrittr", "nnls", "purrr"] 3515 }, 3516 "MIRA": { 3517 "name": "MIRA", 3518 "version": "1.32.0", 3519 "sha256": "0984rwhhz19mc3q7y4cpcz0vzfaiw6n5i4x3qv0412bmivpjp2kh", 3520 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "bsseq", "data_table", "ggplot2"] 3521 }, 3522 "MIRit": { 3523 "name": "MIRit", 3524 "version": "1.6.0", 3525 "sha256": "0mk01yzi4aan6k1bxlpjaiyh3yx8h060pdhgif67hidk8yav9gzk", 3526 "depends": ["AnnotationDbi", "BiocFileCache", "BiocParallel", "DESeq2", "MultiAssayExperiment", "Rcpp", "Rgraphviz", "edgeR", "fgsea", "genekitr", "geneset", "ggplot2", "ggpubr", "graph", "graphite", "httr", "limma", "rlang"] 3527 }, 3528 "MLInterfaces": { 3529 "name": "MLInterfaces", 3530 "version": "1.90.0", 3531 "sha256": "055ppz9d1f5l2ab11zqf1v47d1mvhb97j45wyrr89d822085nml1", 3532 "depends": ["Biobase", "BiocGenerics", "MASS", "RColorBrewer", "Rcpp", "SummarizedExperiment", "annotate", "cluster", "fpc", "gbm", "gdata", "genefilter", "ggvis", "hwriter", "magrittr", "mlbench", "pls", "rpart", "sfsmisc", "shiny", "threejs"] 3533 }, 3534 "MLP": { 3535 "name": "MLP", 3536 "version": "1.58.0", 3537 "sha256": "0q24amdsz4zpwf3vs9xcjbba8a3q4p9g54zqacxmjpd989f1ikvd", 3538 "depends": ["AnnotationDbi", "gplots"] 3539 }, 3540 "MLSeq": { 3541 "name": "MLSeq", 3542 "version": "2.28.0", 3543 "sha256": "0wmygr2ss4h8pjynqa32d53f46sdmglgjcmnr6vifp915f4aa3gj", 3544 "depends": ["Biobase", "DESeq2", "SummarizedExperiment", "VennDiagram", "caret", "edgeR", "foreach", "ggplot2", "limma", "pamr", "plyr", "sSeq", "testthat", "xtable"] 3545 }, 3546 "MMDiff2": { 3547 "name": "MMDiff2", 3548 "version": "1.38.0", 3549 "sha256": "18kj3ddhqwg9x623gfp8zc4mhfhqpi95f571rrfm30hiw1p6s6vr", 3550 "depends": ["BSgenome", "Biobase", "Biostrings", "GenomicRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "ggplot2", "locfit", "shiny"] 3551 }, 3552 "MODA": { 3553 "name": "MODA", 3554 "version": "1.36.0", 3555 "sha256": "19f3nwr7czq7qw6lbmvck312w5dvk8ycad0a4n623r79xccgjs5y", 3556 "depends": ["AMOUNTAIN", "RColorBrewer", "WGCNA", "cluster", "dynamicTreeCut", "igraph"] 3557 }, 3558 "MOFA2": { 3559 "name": "MOFA2", 3560 "version": "1.20.0", 3561 "sha256": "10a13ay9sckaajfqkx79274npiibghk98v717n0xzqxzcx6j7f79", 3562 "depends": ["DelayedArray", "HDF5Array", "RColorBrewer", "Rtsne", "basilisk", "corrplot", "cowplot", "dplyr", "forcats", "ggplot2", "ggrepel", "magrittr", "pheatmap", "reshape2", "reticulate", "rhdf5", "stringi", "tidyr", "uwot"] 3563 }, 3564 "MOGAMUN": { 3565 "name": "MOGAMUN", 3566 "version": "1.20.0", 3567 "sha256": "18qqxgs3qy6r3rksqinck68mkcj1kh2gxrxaqlxd8xbhd0ixri1r", 3568 "depends": ["BiocParallel", "RCy3", "RUnit", "igraph", "stringr"] 3569 }, 3570 "MOMA": { 3571 "name": "MOMA", 3572 "version": "1.22.0", 3573 "sha256": "0306d52fvb98vwaalw786vh1cb0b0swd8pkvbc642cylbb0aq9l2", 3574 "depends": ["ComplexHeatmap", "MKmisc", "MultiAssayExperiment", "RColorBrewer", "circlize", "cluster", "dplyr", "ggplot2", "magrittr", "qvalue", "readr", "reshape2", "rlang", "stringr", "tibble", "tidyr"] 3575 }, 3576 "MOSClip": { 3577 "name": "MOSClip", 3578 "version": "1.4.0", 3579 "sha256": "1a7lkc2v2w12mzfmsakj4398xv7f8bjijsvsvczjglm24dbiijs4", 3580 "depends": ["AnnotationDbi", "ComplexHeatmap", "FactoMineR", "Matrix", "MultiAssayExperiment", "NbClust", "RColorBrewer", "S4Vectors", "SuperExactTest", "checkmate", "circlize", "corpcor", "coxrobust", "elasticnet", "gRbase", "ggplot2", "ggplotify", "graph", "graphite", "gridExtra", "igraph", "org_Hs_eg_db", "pheatmap", "qpgraph", "reshape", "survival", "survminer"] 3581 }, 3582 "MOSim": { 3583 "name": "MOSim", 3584 "version": "2.6.0", 3585 "sha256": "16mq70imxcp1xkvz2dyvzdcm3h1k6l2s1awmlw58ipk0ycsfsx49", 3586 "depends": ["HiddenMarkov", "IRanges", "Rcpp", "S4Vectors", "Seurat", "Signac", "cpp11", "dplyr", "edgeR", "ggplot2", "lazyeval", "matrixStats", "rlang", "scran", "stringi", "stringr", "zoo"] 3587 }, 3588 "MPAC": { 3589 "name": "MPAC", 3590 "version": "1.4.0", 3591 "sha256": "0n7cq12q5p913bca7495lnbcksqiww1vdxg0ysfl0ii39q4189ff", 3592 "depends": ["BiocParallel", "BiocSingular", "ComplexHeatmap", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bluster", "circlize", "data_table", "fgsea", "fitdistrplus", "ggplot2", "ggraph", "igraph", "scales", "scran", "stringr", "survival", "survminer", "viridis"] 3593 }, 3594 "MPFE": { 3595 "name": "MPFE", 3596 "version": "1.46.0", 3597 "sha256": "01v6ick1i5ix7b71glx56fxbal5ndrv5b2yq2lwzxp26wfq28kas", 3598 "depends": [] 3599 }, 3600 "MPRAnalyze": { 3601 "name": "MPRAnalyze", 3602 "version": "1.28.0", 3603 "sha256": "08c6v1lngv3wypl552n95pkhvq6an22g6wpy4dvrmwxg1layjf93", 3604 "depends": ["BiocParallel", "SummarizedExperiment", "progress"] 3605 }, 3606 "MSA2dist": { 3607 "name": "MSA2dist", 3608 "version": "1.14.0", 3609 "sha256": "1rdqnk8l2b2p69yyvfa9ybv0ghxz2qks5rnczg10brmksf50g749", 3610 "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rcpp", "RcppThread", "ape", "doParallel", "dplyr", "foreach", "pwalign", "rlang", "seqinr", "stringi", "stringr", "tibble", "tidyr"] 3611 }, 3612 "MSPrep": { 3613 "name": "MSPrep", 3614 "version": "1.19.0", 3615 "sha256": "14n0f8rcx8fdn0w07wvbkprk3z31dfac6z8q7c50j0rp2xax9b69", 3616 "depends": ["S4Vectors", "SummarizedExperiment", "VIM", "crmn", "dplyr", "magrittr", "missForest", "pcaMethods", "preprocessCore", "rlang", "stringr", "sva", "tibble", "tidyr"] 3617 }, 3618 "MSnID": { 3619 "name": "MSnID", 3620 "version": "1.44.0", 3621 "sha256": "1spb72pc7idn597sb8qywynf6sg306p8vbdbd0gcib1q1vinzqy0", 3622 "depends": ["AnnotationDbi", "AnnotationHub", "Biobase", "BiocGenerics", "BiocStyle", "Biostrings", "MSnbase", "ProtGenerics", "RUnit", "R_cache", "Rcpp", "data_table", "doParallel", "dplyr", "foreach", "ggplot2", "iterators", "msmsTests", "mzID", "mzR", "purrr", "reshape2", "rlang", "stringr", "tibble", "xtable"] 3623 }, 3624 "MSnbase": { 3625 "name": "MSnbase", 3626 "version": "2.36.0", 3627 "sha256": "0k7diyzr92pjgia639w1c58km78pr199ajk0i72y4x1zbhx82c8v", 3628 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "IRanges", "MALDIquant", "MASS", "MsCoreUtils", "PSMatch", "ProtGenerics", "Rcpp", "S4Vectors", "affy", "digest", "ggplot2", "impute", "lattice", "mzID", "mzR", "pcaMethods", "plyr", "scales", "vsn"] 3629 }, 3630 "MSstats": { 3631 "name": "MSstats", 3632 "version": "4.18.0", 3633 "sha256": "084275gir4sndjwx40qn642k1jian24xkby30x1ld7b378nsnmmf", 3634 "depends": ["MASS", "MSstatsConvert", "Rcpp", "RcppArmadillo", "checkmate", "data_table", "ggplot2", "ggrepel", "gplots", "htmltools", "limma", "lme4", "marray", "plotly", "preprocessCore", "rlang", "statmod", "survival"] 3635 }, 3636 "MSstatsBig": { 3637 "name": "MSstatsBig", 3638 "version": "1.8.0", 3639 "sha256": "12hd5a0s1yfyzxmnrhpa8xicy5232m947d6gmqy4s6pfgi0mjzbs", 3640 "depends": ["DBI", "MSstats", "MSstatsConvert", "arrow", "dplyr", "readr", "sparklyr"] 3641 }, 3642 "MSstatsBioNet": { 3643 "name": "MSstatsBioNet", 3644 "version": "1.2.0", 3645 "sha256": "0vaxm03xhzsvirkmzblg6qw89rxgi6g7w60csh1yyp08zcqhpmli", 3646 "depends": ["MSstats", "RCy3", "httr", "jsonlite", "r2r", "tidyr"] 3647 }, 3648 "MSstatsConvert": { 3649 "name": "MSstatsConvert", 3650 "version": "1.20.0", 3651 "sha256": "0f8rf7mniv3r30910ilhnrcaffmqddkp4n4syq9aqdn7fl630s0b", 3652 "depends": ["Rcpp", "checkmate", "data_table", "log4r", "stringi"] 3653 }, 3654 "MSstatsLOBD": { 3655 "name": "MSstatsLOBD", 3656 "version": "1.18.0", 3657 "sha256": "00czbv3rsg3nnwhvjwl27vm9bcywmmg7y16qnwjpx7hzdsznpyik", 3658 "depends": ["Rcpp", "ggplot2", "minpack_lm"] 3659 }, 3660 "MSstatsLiP": { 3661 "name": "MSstatsLiP", 3662 "version": "1.16.0", 3663 "sha256": "19441shsymqvxzgkj0n1ypyga43514q06cphfyrhy6zcja0zrlcs", 3664 "depends": ["Biostrings", "MSstats", "MSstatsConvert", "MSstatsPTM", "Rcpp", "checkmate", "data_table", "dplyr", "factoextra", "ggplot2", "ggpubr", "gridExtra", "htmltools", "plotly", "purrr", "scales", "stringr", "tibble", "tidyr", "tidyverse"] 3665 }, 3666 "MSstatsPTM": { 3667 "name": "MSstatsPTM", 3668 "version": "2.12.0", 3669 "sha256": "063q6bj0caxihnx9s66s0rkw9fxfhra53hfg0bfwd1iydgf10294", 3670 "depends": ["Biostrings", "MSstats", "MSstatsConvert", "MSstatsTMT", "Rcpp", "checkmate", "data_table", "dplyr", "ggplot2", "ggrepel", "gridExtra", "htmltools", "plotly", "stringi", "stringr"] 3671 }, 3672 "MSstatsQC": { 3673 "name": "MSstatsQC", 3674 "version": "2.28.0", 3675 "sha256": "1672v4xgb108idm82n125sm048knaahp41msmwhjrrl59v7w7nw7", 3676 "depends": ["MSnbase", "dplyr", "ggExtra", "ggplot2", "plotly", "qcmetrics"] 3677 }, 3678 "MSstatsQCgui": { 3679 "name": "MSstatsQCgui", 3680 "version": "1.30.0", 3681 "sha256": "0n10hkb5yds7jbv2q0p59rkia210y38frc5s49bb3z0mm1mg4kbb", 3682 "depends": ["MSstatsQC", "dplyr", "ggExtra", "gridExtra", "plotly", "shiny"] 3683 }, 3684 "MSstatsResponse": { 3685 "name": "MSstatsResponse", 3686 "version": "1.0.0", 3687 "sha256": "1cbgkszjy7ywrdl31swi31yd8ndbkdz9k5wnxylfq1yii15yal03", 3688 "depends": ["BiocParallel", "data_table", "dplyr", "ggplot2"] 3689 }, 3690 "MSstatsShiny": { 3691 "name": "MSstatsShiny", 3692 "version": "1.12.0", 3693 "sha256": "0hrym0l2jwr0hvlnkmbxvpfyjn9jdxddyq2abvzq597liw8x5r26", 3694 "depends": ["DT", "Hmisc", "MSstats", "MSstatsBioNet", "MSstatsConvert", "MSstatsPTM", "MSstatsTMT", "arrow", "data_table", "dplyr", "ggplot2", "ggrepel", "gplots", "htmltools", "marray", "mockery", "plotly", "readxl", "shiny", "shinyBS", "shinybusy", "shinydashboard", "shinyjs", "tidyr", "uuid"] 3695 }, 3696 "MSstatsTMT": { 3697 "name": "MSstatsTMT", 3698 "version": "2.18.0", 3699 "sha256": "020h4w7xph1b4fzmhpwg2dxz0lx87ml17h9wlbabgixys9jrs4hq", 3700 "depends": ["MSstats", "MSstatsConvert", "checkmate", "data_table", "ggplot2", "htmltools", "limma", "lme4", "lmerTest", "plotly"] 3701 }, 3702 "MVCClass": { 3703 "name": "MVCClass", 3704 "version": "1.84.0", 3705 "sha256": "05piqhv4dfwal0kws0qvdn14r1w5i2sx6wlgqr08w1wzf1cf3wvq", 3706 "depends": [] 3707 }, 3708 "MWASTools": { 3709 "name": "MWASTools", 3710 "version": "1.34.0", 3711 "sha256": "16d1vkw3wl9mspbfgsyzwpz1pz1krlz8g9g3159qqfmh7fwlwqpm", 3712 "depends": ["ComplexHeatmap", "KEGGREST", "KEGGgraph", "RCurl", "SummarizedExperiment", "boot", "car", "ggplot2", "glm2", "gridExtra", "igraph", "ppcor", "qvalue"] 3713 }, 3714 "MantelCorr": { 3715 "name": "MantelCorr", 3716 "version": "1.80.0", 3717 "sha256": "1da839dpy6v14fc7kgn54n107y957xw7vvv5zkw10pd1x9nmrkaz", 3718 "depends": [] 3719 }, 3720 "MassArray": { 3721 "name": "MassArray", 3722 "version": "1.62.0", 3723 "sha256": "1kzxrq4f7fi3q538zq0pbn7s28mdh0fp9l8ipgwfdyiwkhsmp4i2", 3724 "depends": [] 3725 }, 3726 "MassSpecWavelet": { 3727 "name": "MassSpecWavelet", 3728 "version": "1.76.0", 3729 "sha256": "08fv8mqhld2xpbyk4yzmb4w01jcg1fiwa14p703admwx0kfly9kv", 3730 "depends": [] 3731 }, 3732 "MatrixGenerics": { 3733 "name": "MatrixGenerics", 3734 "version": "1.22.0", 3735 "sha256": "0yjm21hnzvdffq6xg2viabh3jamb0cb0rycplbhfdqf7k8ycngdm", 3736 "depends": ["matrixStats"] 3737 }, 3738 "MatrixQCvis": { 3739 "name": "MatrixQCvis", 3740 "version": "1.18.0", 3741 "sha256": "1v2vx6vlk6s7i1zb3h24wq3hnqffi9fwf93fibcwsfzl2kdwf9bi", 3742 "depends": ["ComplexHeatmap", "DT", "ExperimentHub", "Hmisc", "MASS", "Rtsne", "SummarizedExperiment", "UpSetR", "dplyr", "ggplot2", "htmlwidgets", "impute", "imputeLCMD", "limma", "pcaMethods", "plotly", "proDA", "rlang", "rmarkdown", "shiny", "shinydashboard", "shinyhelper", "shinyjs", "sva", "tibble", "tidyr", "umap", "vsn"] 3743 }, 3744 "MatrixRider": { 3745 "name": "MatrixRider", 3746 "version": "1.42.0", 3747 "sha256": "11nqdvaxnf49i57lf3gd3xcni6ybhjxsxsm0m1w0xl1isgvc451m", 3748 "depends": ["Biostrings", "IRanges", "S4Vectors", "TFBSTools", "XVector"] 3749 }, 3750 "MeSHDbi": { 3751 "name": "MeSHDbi", 3752 "version": "1.46.0", 3753 "sha256": "1cxigmicaxqjrg8n36v2db4a806j8qx3iank7r17hxgniq5q8zh4", 3754 "depends": ["AnnotationDbi", "Biobase", "RSQLite"] 3755 }, 3756 "MeasurementError_cor": { 3757 "name": "MeasurementError.cor", 3758 "version": "1.82.0", 3759 "sha256": "1hkpa8wisx29cz8n5m1w0vb7nbz1vbxpca6m3zja245zi6ifqbz9", 3760 "depends": [] 3761 }, 3762 "Mergeomics": { 3763 "name": "Mergeomics", 3764 "version": "1.38.0", 3765 "sha256": "0gvcvxh7aycmq5svwmn9vxjibcgpksv28irgal2m101vsjngmzx8", 3766 "depends": [] 3767 }, 3768 "MesKit": { 3769 "name": "MesKit", 3770 "version": "1.20.0", 3771 "sha256": "1x1s2ylbjd6mbq6498sj992ik44ipyi4rpnwwd4nj3q212dcx9wf", 3772 "depends": ["AnnotationDbi", "Biostrings", "ComplexHeatmap", "IRanges", "RColorBrewer", "S4Vectors", "ape", "circlize", "cowplot", "data_table", "dplyr", "ggplot2", "ggrepel", "ggridges", "mclust", "phangorn", "pracma", "tidyr"] 3773 }, 3774 "MetCirc": { 3775 "name": "MetCirc", 3776 "version": "1.40.0", 3777 "sha256": "15zwkgwqnpndlpw9pqd5mkfbmcdb1aa331fvkkhxzdgcd5zq7a49", 3778 "depends": ["MsCoreUtils", "S4Vectors", "Spectra", "amap", "circlize", "ggplot2", "scales", "shiny"] 3779 }, 3780 "MetID": { 3781 "name": "MetID", 3782 "version": "1.28.0", 3783 "sha256": "1xh0y6k6ik9nzy1wrzfr8b255194b26jibflgdi4vzn3hbm2z30p", 3784 "depends": ["ChemmineR", "Matrix", "devtools", "igraph", "stringr"] 3785 }, 3786 "MetNet": { 3787 "name": "MetNet", 3788 "version": "1.28.0", 3789 "sha256": "0wj31qhyg0yn1cviprn3y6411rgl5sj0ns4iin3qc53qf4ypjspc", 3790 "depends": ["BiocParallel", "GENIE3", "GeneNet", "S4Vectors", "SummarizedExperiment", "bnlearn", "corpcor", "dplyr", "ggplot2", "parmigene", "psych", "rlang", "stabs", "tibble", "tidyr"] 3791 }, 3792 "MetaCyto": { 3793 "name": "MetaCyto", 3794 "version": "1.32.0", 3795 "sha256": "1km53r657jfjipiq88nir9s6qwdl4c1mw8mldhimdy8hm6kf7mqx", 3796 "depends": ["FlowSOM", "cluster", "fastcluster", "flowCore", "ggplot2", "metafor", "tidyr"] 3797 }, 3798 "MetaDICT": { 3799 "name": "MetaDICT", 3800 "version": "1.0.0", 3801 "sha256": "00afs37df59wc0yjxd3diskcxfyc2zjcv5nycvr5sv8bizlh0cx5", 3802 "depends": ["RANN", "ape", "cluster", "ecodist", "edgeR", "ggplot2", "ggpubr", "igraph", "matrixStats", "vegan", "viridis"] 3803 }, 3804 "MetaNeighbor": { 3805 "name": "MetaNeighbor", 3806 "version": "1.29.0", 3807 "sha256": "0fvsnwwpvwbdcq7lgbb2jq9n6scr33ip3s3z14v6nxm7zmf6i5bn", 3808 "depends": ["Matrix", "RColorBrewer", "SingleCellExperiment", "SummarizedExperiment", "beanplot", "dplyr", "ggplot2", "gplots", "igraph", "matrixStats", "tibble", "tidyr"] 3809 }, 3810 "MetaPhOR": { 3811 "name": "MetaPhOR", 3812 "version": "1.12.0", 3813 "sha256": "1lwb3ksf0yrdwzv9b0azcnn2fng4vrkwls3ds8bqaq6bn2n3pkxk", 3814 "depends": ["RCy3", "RecordLinkage", "clusterProfiler", "ggplot2", "ggrepel", "pheatmap", "stringr"] 3815 }, 3816 "MetaboAnnotation": { 3817 "name": "MetaboAnnotation", 3818 "version": "1.14.0", 3819 "sha256": "07b72g2l2j16a3q6cl3fnpjk2v0iw92c1jb21hyhrs9lxvalsvqz", 3820 "depends": ["AnnotationHub", "BiocGenerics", "BiocParallel", "CompoundDb", "MetaboCoreUtils", "MsCoreUtils", "ProtGenerics", "QFeatures", "S4Vectors", "Spectra", "SummarizedExperiment"] 3821 }, 3822 "MetaboCoreUtils": { 3823 "name": "MetaboCoreUtils", 3824 "version": "1.18.0", 3825 "sha256": "1ddcbr3lhi6pbb5mv2h41vgv26z9jncw1wbw5iq8dqhk09f9k1kn", 3826 "depends": ["BiocParallel", "MsCoreUtils"] 3827 }, 3828 "MetaboDynamics": { 3829 "name": "MetaboDynamics", 3830 "version": "2.0.0", 3831 "sha256": "1xba89ira24vlidx9cf0rp6jjc3kfl4b324n8z1bpixzsnjqrw7h", 3832 "depends": ["BH", "KEGGREST", "Rcpp", "RcppEigen", "RcppParallel", "S4Vectors", "StanHeaders", "SummarizedExperiment", "ape", "dplyr", "dynamicTreeCut", "ggplot2", "ggtree", "patchwork", "rlang", "rstan", "rstantools", "stringr", "tidyr"] 3833 }, 3834 "MetaboSignal": { 3835 "name": "MetaboSignal", 3836 "version": "1.40.0", 3837 "sha256": "07lxxxxn3h2ilrg436dgq0754s1xkkz9md91j89jwv0h4kpr22vj", 3838 "depends": ["AnnotationDbi", "EnsDb_Hsapiens_v75", "KEGGREST", "KEGGgraph", "MWASTools", "RCurl", "biomaRt", "hpar", "igraph", "mygene", "org_Hs_eg_db"] 3839 }, 3840 "MethPed": { 3841 "name": "MethPed", 3842 "version": "1.38.0", 3843 "sha256": "18ld9iq0kxzc2igran2jr8w3jrj1k73p5i0lx8dgl58kdbg18ycj", 3844 "depends": ["Biobase", "randomForest"] 3845 }, 3846 "MethReg": { 3847 "name": "MethReg", 3848 "version": "1.20.0", 3849 "sha256": "049cs12928mfmllqrrywmdk956ai7wsgxf4k093mh810g3qg1fwb", 3850 "depends": ["AnnotationHub", "DelayedArray", "ExperimentHub", "GenomicRanges", "IRanges", "JASPAR2024", "MASS", "Matrix", "RSQLite", "S4Vectors", "SummarizedExperiment", "TFBSTools", "dplyr", "ggplot2", "ggpubr", "openxlsx", "plyr", "progress", "pscl", "readr", "rlang", "sesame", "sesameData", "sfsmisc", "stringr", "tibble", "tidyr"] 3851 }, 3852 "MethTargetedNGS": { 3853 "name": "MethTargetedNGS", 3854 "version": "1.42.0", 3855 "sha256": "0mjq3q8q43p5gni40z5xlkhgpdxnphwi8xjrqc9gjwwqbra5986l", 3856 "depends": ["Biostrings", "gplots", "pwalign", "seqinr", "stringr"] 3857 }, 3858 "MethylAid": { 3859 "name": "MethylAid", 3860 "version": "1.44.0", 3861 "sha256": "1gg6wy7g583i348mvd9qww5pnjkn8g0ckkdkwf463kgs12483n2n", 3862 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "RColorBrewer", "SummarizedExperiment", "ggplot2", "gridBase", "hexbin", "matrixStats", "minfi", "shiny"] 3863 }, 3864 "MethylMix": { 3865 "name": "MethylMix", 3866 "version": "2.40.0", 3867 "sha256": "1wdmq8jdnd37wrasdrfmy6xskpw2h6w2g3a514f0zn3m3fc7wpqv", 3868 "depends": ["RColorBrewer", "RCurl", "RPMM", "R_matlab", "data_table", "digest", "foreach", "ggplot2", "impute", "limma"] 3869 }, 3870 "MethylSeekR": { 3871 "name": "MethylSeekR", 3872 "version": "1.50.0", 3873 "sha256": "00i0g5xxdd7xf268nqsl76im6d5za3h9apx2dsdyvjdrkn8shg98", 3874 "depends": ["BSgenome", "GenomeInfoDb", "GenomicRanges", "IRanges", "geneplotter", "mhsmm", "rtracklayer"] 3875 }, 3876 "Mfuzz": { 3877 "name": "Mfuzz", 3878 "version": "2.70.0", 3879 "sha256": "0fjdfhj340fbv9m18a5hlsd8g7n9zdrn4h6h4fsa3pmzmj06x7l5", 3880 "depends": ["Biobase", "e1071", "tkWidgets"] 3881 }, 3882 "MiChip": { 3883 "name": "MiChip", 3884 "version": "1.64.0", 3885 "sha256": "0bjvg2jyfif03vx53xznhdnmx2s4nfv05l6kbq907rv84ji692b8", 3886 "depends": ["Biobase"] 3887 }, 3888 "MiPP": { 3889 "name": "MiPP", 3890 "version": "1.82.0", 3891 "sha256": "0y8dcf69c39capj45j276dhlcjxwvxny5bb5w4w9gp2l4gm3nraq", 3892 "depends": ["Biobase", "MASS", "e1071"] 3893 }, 3894 "MiRaGE": { 3895 "name": "MiRaGE", 3896 "version": "1.52.0", 3897 "sha256": "0zl37d9adbra11ma4pra78w76vfdli1ljs8sv729dyn2h2vmjh1q", 3898 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocManager", "S4Vectors"] 3899 }, 3900 "MicrobiomeProfiler": { 3901 "name": "MicrobiomeProfiler", 3902 "version": "1.16.0", 3903 "sha256": "0qqv2vkag5a3rp2wcf3kxk99dwymd0p828g12v301d65g5jzlp93", 3904 "depends": ["DT", "clusterProfiler", "config", "enrichplot", "ggplot2", "golem", "gson", "htmltools", "magrittr", "shiny", "shinyWidgets", "shinycustomloader", "yulab_utils"] 3905 }, 3906 "MicrobiotaProcess": { 3907 "name": "MicrobiotaProcess", 3908 "version": "1.22.0", 3909 "sha256": "0lf3z2pcvvy905qanm2a7ryr2kb74rnghmn2ghq0669hqgdihh0x", 3910 "depends": ["Biostrings", "MASS", "SummarizedExperiment", "ape", "cli", "coin", "data_table", "dplyr", "dtplyr", "foreach", "ggfun", "ggplot2", "ggrepel", "ggsignif", "ggstar", "ggtree", "ggtreeExtra", "magrittr", "patchwork", "pillar", "plyr", "rlang", "tibble", "tidyr", "tidyselect", "tidytree", "treeio", "vegan", "zoo"] 3911 }, 3912 "MineICA": { 3913 "name": "MineICA", 3914 "version": "1.49.0", 3915 "sha256": "0fnlyrx6a1m8l2zqphlkdsqdkcl4h5mv2fan0ig23k0qcv7cxyzs", 3916 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GOstats", "Hmisc", "JADE", "RColorBrewer", "Rgraphviz", "annotate", "biomaRt", "cluster", "colorspace", "fastICA", "foreach", "fpc", "ggplot2", "graph", "gtools", "igraph", "lumi", "lumiHumanAll_db", "marray", "mclust", "plyr", "scales", "xtable"] 3917 }, 3918 "MinimumDistance": { 3919 "name": "MinimumDistance", 3920 "version": "1.54.0", 3921 "sha256": "15s7a7w78p29a4a8p408r887pnl3l6wcsj1zjh0hjwvirn13v4hi", 3922 "depends": ["Biobase", "BiocGenerics", "DNAcopy", "GenomicRanges", "IRanges", "MatrixGenerics", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VanillaICE", "data_table", "ff", "foreach", "lattice", "matrixStats", "oligoClasses"] 3923 }, 3924 "ModCon": { 3925 "name": "ModCon", 3926 "version": "1.18.0", 3927 "sha256": "0vg663nhmj1xmxh7bi5v9z0rcps3bl7qs6v6dd7wp6ybv8vkr5g1", 3928 "depends": ["data_table"] 3929 }, 3930 "Modstrings": { 3931 "name": "Modstrings", 3932 "version": "1.26.0", 3933 "sha256": "1apgx7jf02y7v3rd36y3r3fsl41pg2ajxq9cmi4nrnpf0s1jq1f2", 3934 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "XVector", "crayon", "stringi", "stringr"] 3935 }, 3936 "MoleculeExperiment": { 3937 "name": "MoleculeExperiment", 3938 "version": "1.10.0", 3939 "sha256": "0g30rqj98dagyxl7wl84imszrb7fh0c0cd2g41x1spviirwga1zm", 3940 "depends": ["BiocParallel", "EBImage", "Matrix", "S4Vectors", "SpatialExperiment", "cli", "data_table", "dplyr", "ggplot2", "magrittr", "purrr", "rhdf5", "rjson", "rlang", "terra"] 3941 }, 3942 "Moonlight2R": { 3943 "name": "Moonlight2R", 3944 "version": "1.8.0", 3945 "sha256": "0x8w3qgm0k7pq2kyc7y6nqsbdfwqg68ki6bm1vvgx0wpgy9zza86", 3946 "depends": ["AnnotationHub", "Biobase", "BiocGenerics", "ComplexHeatmap", "DOSE", "EpiMix", "ExperimentHub", "GEOquery", "GenomicRanges", "HiveR", "RColorBrewer", "RISmed", "circlize", "clusterProfiler", "data_table", "doParallel", "dplyr", "easyPubMed", "foreach", "fuzzyjoin", "ggplot2", "gplots", "magrittr", "org_Hs_eg_db", "parmigene", "purrr", "qpdf", "randomForest", "readr", "rlang", "rtracklayer", "seqminer", "stringr", "tibble", "tidyHeatmap", "tidyr", "withr"] 3947 }, 3948 "MoonlightR": { 3949 "name": "MoonlightR", 3950 "version": "1.36.0", 3951 "sha256": "1mlg7aczp8wafdmwjq9znra80w8h469dvsiqqpf5bhhbq8lax7qp", 3952 "depends": ["Biobase", "DOSE", "GEOquery", "HiveR", "RColorBrewer", "RISmed", "SummarizedExperiment", "TCGAbiolinks", "circlize", "clusterProfiler", "doParallel", "foreach", "gplots", "limma", "parmigene", "randomForest"] 3953 }, 3954 "Motif2Site": { 3955 "name": "Motif2Site", 3956 "version": "1.14.0", 3957 "sha256": "1jgdh9gqlm0lydgk1l1946fhnb2ma8v63841bzaj3bw8j4876vjh", 3958 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "edgeR", "mixtools"] 3959 }, 3960 "MotifDb": { 3961 "name": "MotifDb", 3962 "version": "1.52.0", 3963 "sha256": "01ps2pn7qv4v9f88z74mbj4293yamaa0mssaaai92knjvzc8fs2w", 3964 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "rtracklayer", "splitstackshape"] 3965 }, 3966 "MotifPeeker": { 3967 "name": "MotifPeeker", 3968 "version": "1.2.0", 3969 "sha256": "0s16b0zpksm52w6kszhah6shrh69wxww847qq1fv9xrmrg8zryax", 3970 "depends": ["BSgenome", "BiocFileCache", "BiocParallel", "Biostrings", "DT", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "dplyr", "ggplot2", "heatmaply", "htmltools", "htmlwidgets", "memes", "plotly", "purrr", "rmarkdown", "rtracklayer", "tidyr", "universalmotif", "viridis"] 3971 }, 3972 "MouseFM": { 3973 "name": "MouseFM", 3974 "version": "1.20.0", 3975 "sha256": "1kyagqg0rs5pzqqjn8fsdbmkaj9vzq6jqvrmyjswibxdasgy8vwm", 3976 "depends": ["GenomicRanges", "IRanges", "Seqinfo", "biomaRt", "curl", "data_table", "dplyr", "ggplot2", "gtools", "httr", "jsonlite", "reshape2", "rlist", "scales", "tidyr"] 3977 }, 3978 "MsBackendMassbank": { 3979 "name": "MsBackendMassbank", 3980 "version": "1.18.0", 3981 "sha256": "06ac38fshnn1ra0k3dmmrlsc6036sx5kzb84h8j9k1j336ra3lm1", 3982 "depends": ["BiocParallel", "DBI", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra"] 3983 }, 3984 "MsBackendMetaboLights": { 3985 "name": "MsBackendMetaboLights", 3986 "version": "1.4.0", 3987 "sha256": "1iniryzmqwbkwdxrax432hzndda81g5a7jylkm8579n872rl24cj", 3988 "depends": ["BiocFileCache", "ProtGenerics", "S4Vectors", "Spectra", "curl", "progress"] 3989 }, 3990 "MsBackendMgf": { 3991 "name": "MsBackendMgf", 3992 "version": "1.18.0", 3993 "sha256": "0hycd0jj3bc5h3lcgxpm6ysy2mzk3jp0rxq1hrgyqpz1s9zigbsy", 3994 "depends": ["BiocParallel", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra"] 3995 }, 3996 "MsBackendMsp": { 3997 "name": "MsBackendMsp", 3998 "version": "1.14.0", 3999 "sha256": "1mqrn6kq6hrnymv80ypls7mmpzjh0zy3b44d1ayikm5ilyg57dki", 4000 "depends": ["BiocParallel", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra"] 4001 }, 4002 "MsBackendRawFileReader": { 4003 "name": "MsBackendRawFileReader", 4004 "version": "1.16.0", 4005 "sha256": "1169db99imv14brygihhfmb1qc3cmhmlwqi5snj5fc8vk46y59c1", 4006 "depends": ["BiocParallel", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra", "rawrr"] 4007 }, 4008 "MsBackendSql": { 4009 "name": "MsBackendSql", 4010 "version": "1.10.0", 4011 "sha256": "1h0pbk4wkiri36qdmln7v0wglgpx5lhbnrv6q903j2x8nhjhgffx", 4012 "depends": ["BiocGenerics", "BiocParallel", "DBI", "IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra", "data_table", "fastmatch", "progress", "stringi"] 4013 }, 4014 "MsCoreUtils": { 4015 "name": "MsCoreUtils", 4016 "version": "1.21.0", 4017 "sha256": "1lckbd96589vsmyy6prqijxafwiwx3mnm9c1jlw6dbxivfzmk3n7", 4018 "depends": ["MASS", "Rcpp", "S4Vectors", "clue"] 4019 }, 4020 "MsDataHub": { 4021 "name": "MsDataHub", 4022 "version": "1.10.0", 4023 "sha256": "09rfj583b1vz3p328pnlrzj7mxg6804ia1q84p9y5pvzcb0z17fv", 4024 "depends": ["ExperimentHub"] 4025 }, 4026 "MsExperiment": { 4027 "name": "MsExperiment", 4028 "version": "1.12.0", 4029 "sha256": "1braagzs450sxbh29rdh0dck7pwi49wd45rx3j36fw4720hgcilb", 4030 "depends": ["BiocGenerics", "DBI", "IRanges", "ProtGenerics", "QFeatures", "S4Vectors", "Spectra", "SummarizedExperiment"] 4031 }, 4032 "MsFeatures": { 4033 "name": "MsFeatures", 4034 "version": "1.18.0", 4035 "sha256": "14cm8mmqgj1pf96fdkwasr8zfpyrpz9p8kfnq5n3srh9qnfsvyk7", 4036 "depends": ["MsCoreUtils", "ProtGenerics", "SummarizedExperiment"] 4037 }, 4038 "MsQuality": { 4039 "name": "MsQuality", 4040 "version": "1.10.0", 4041 "sha256": "07cb36mrz11r6hpl5cwk3a5myagmslxik0jis8rxbsihkmilpb2r", 4042 "depends": ["BiocParallel", "MsExperiment", "ProtGenerics", "Spectra", "ggplot2", "htmlwidgets", "msdata", "plotly", "rlang", "rmzqc", "shiny", "shinydashboard", "stringr", "tibble", "tidyr"] 4043 }, 4044 "MuData": { 4045 "name": "MuData", 4046 "version": "1.14.0", 4047 "sha256": "0b6289ladkm5c70i4rkw3hc7kxf038n3ryjs9fr44rb1q4mq940n", 4048 "depends": ["DelayedArray", "Matrix", "MultiAssayExperiment", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "rhdf5"] 4049 }, 4050 "Mulcom": { 4051 "name": "Mulcom", 4052 "version": "1.60.0", 4053 "sha256": "1wy30yl3wl1a42mn447dsrlsswi55y00f3rrzpfyv85ap8sx2imw", 4054 "depends": ["Biobase", "fields"] 4055 }, 4056 "MultiAssayExperiment": { 4057 "name": "MultiAssayExperiment", 4058 "version": "1.36.0", 4059 "sha256": "1idng7dc4fx0zn51r43vbxyyl2011y5bznzm4id8nv52zpknd753", 4060 "depends": ["Biobase", "BiocBaseUtils", "BiocGenerics", "DelayedArray", "GenomicRanges", "IRanges", "MatrixGenerics", "S4Vectors", "SummarizedExperiment", "tidyr"] 4061 }, 4062 "MultiBaC": { 4063 "name": "MultiBaC", 4064 "version": "1.20.0", 4065 "sha256": "1cwf0aja5qydbhc7iws09hd9wc4jm98fj0snai59ymgb7vrs08zb", 4066 "depends": ["Matrix", "MultiAssayExperiment", "ggplot2", "pcaMethods", "plotrix", "ropls"] 4067 }, 4068 "MultiDataSet": { 4069 "name": "MultiDataSet", 4070 "version": "1.38.0", 4071 "sha256": "06dgh6zvcz6d1yghys126mkjxmibdf4asn1n2ddmf8bxk500zl5i", 4072 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "ggplot2", "ggrepel", "limma", "qqman"] 4073 }, 4074 "MultiMed": { 4075 "name": "MultiMed", 4076 "version": "2.32.0", 4077 "sha256": "0pn5bavnq3gsyln89p6zrwn44147c9wjpkc04drk65hv9329yh3q", 4078 "depends": [] 4079 }, 4080 "MultiRNAflow": { 4081 "name": "MultiRNAflow", 4082 "version": "1.8.0", 4083 "sha256": "0h4jy154jq7g76a7bnirmpi7rjzzfdslw54sdzzrd7shr3amg4wd", 4084 "depends": ["Biobase", "ComplexHeatmap", "DESeq2", "FactoMineR", "Mfuzz", "S4Vectors", "SummarizedExperiment", "UpSetR", "factoextra", "ggalluvial", "ggplot2", "ggplotify", "ggrepel", "gprofiler2", "plot3D", "plot3Drgl", "reshape2", "rlang"] 4085 }, 4086 "MultimodalExperiment": { 4087 "name": "MultimodalExperiment", 4088 "version": "1.10.0", 4089 "sha256": "1dv4bq17p1jwk4ympjd7902wmbqp641s87c8kdkr0c7qx5q7ibdj", 4090 "depends": ["BiocGenerics", "IRanges", "MultiAssayExperiment", "S4Vectors"] 4091 }, 4092 "MungeSumstats": { 4093 "name": "MungeSumstats", 4094 "version": "1.18.0", 4095 "sha256": "0g2995z6gj0xrn45bvjpvnlp9cd9iwxq8hwvl4lfvaij1qqlv7i7", 4096 "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "RCurl", "R_utils", "VariantAnnotation", "data_table", "dplyr", "ieugwasr", "rtracklayer", "stringr"] 4097 }, 4098 "MutationalPatterns": { 4099 "name": "MutationalPatterns", 4100 "version": "3.19.1", 4101 "sha256": "1y7yxricvivg3ds3jacwf5qb366xvzw8sff9wddigz8p5kyzs7f6", 4102 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "NMF", "RColorBrewer", "S4Vectors", "Seqinfo", "VariantAnnotation", "cowplot", "dplyr", "ggalluvial", "ggdendro", "ggplot2", "magrittr", "pracma", "purrr", "stringr", "tibble", "tidyr"] 4103 }, 4104 "NADfinder": { 4105 "name": "NADfinder", 4106 "version": "1.34.0", 4107 "sha256": "19gg4g815zgpphamvnyg6xk2jz47gwb49rr6inqz8l304a6ibsca", 4108 "depends": ["ATACseqQC", "BiocGenerics", "EmpiricalBrownsMethod", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "baseline", "corrplot", "csaw", "limma", "metap", "rtracklayer", "signal", "trackViewer"] 4109 }, 4110 "NBAMSeq": { 4111 "name": "NBAMSeq", 4112 "version": "1.26.0", 4113 "sha256": "0n19b7i3j0465gn41jyrdilgp6rwr3anzfa79l62z4l0ywkjld6r", 4114 "depends": ["BiocParallel", "DESeq2", "S4Vectors", "SummarizedExperiment", "genefilter", "mgcv"] 4115 }, 4116 "NCIgraph": { 4117 "name": "NCIgraph", 4118 "version": "1.58.0", 4119 "sha256": "1vaf53lx2nrcnk45gbwr5whvy9a3ma2zdb8lqym1jp9hs1s1gn9q", 4120 "depends": ["KEGGgraph", "RBGL", "RCy3", "R_oo", "graph"] 4121 }, 4122 "NOISeq": { 4123 "name": "NOISeq", 4124 "version": "2.54.0", 4125 "sha256": "05398q8cqywbvrqgzp9gjyjkv7dlq2v8f3w9rgz60jwma76vdxdw", 4126 "depends": ["Biobase", "Matrix"] 4127 }, 4128 "NPARC": { 4129 "name": "NPARC", 4130 "version": "1.22.0", 4131 "sha256": "0iqmyf0bambl9dp1kypvcxfglvpryy61925zf9hhkapv7wj90v4j", 4132 "depends": ["BiocParallel", "MASS", "broom", "dplyr", "magrittr", "rlang", "tidyr"] 4133 }, 4134 "NTW": { 4135 "name": "NTW", 4136 "version": "1.60.0", 4137 "sha256": "1rsg8294jr134gv01f7y2542ld595740agazr0661vsd18p0any5", 4138 "depends": ["mvtnorm"] 4139 }, 4140 "NanoMethViz": { 4141 "name": "NanoMethViz", 4142 "version": "3.6.0", 4143 "sha256": "1rksk701jpck7ahphb11qrrz9a4hfc59sqlp8yprbjl9cz1pim69", 4144 "depends": ["AnnotationDbi", "BiocSingular", "Biostrings", "GenomicRanges", "IRanges", "R_utils", "Rcpp", "Rsamtools", "S4Vectors", "SummarizedExperiment", "assertthat", "bsseq", "cli", "cpp11", "dbscan", "dplyr", "e1071", "forcats", "fs", "ggplot2", "ggrastr", "glue", "limma", "patchwork", "purrr", "readr", "rlang", "scales", "stringr", "tibble", "tidyr", "withr"] 4145 }, 4146 "NanoStringDiff": { 4147 "name": "NanoStringDiff", 4148 "version": "1.40.0", 4149 "sha256": "0mcnch09brr8c1kfmq6scv04gdxz02a0s8zi1v6xmqr151abkwng", 4150 "depends": ["Biobase", "Rcpp", "matrixStats"] 4151 }, 4152 "NanoStringNCTools": { 4153 "name": "NanoStringNCTools", 4154 "version": "1.18.0", 4155 "sha256": "0l9rbm6b5k13jbf1jmwyiscg81rwkmxir4vidq1pdw53gmxf4mnx", 4156 "depends": ["Biobase", "BiocGenerics", "Biostrings", "IRanges", "RColorBrewer", "S4Vectors", "ggbeeswarm", "ggiraph", "ggplot2", "ggthemes", "pheatmap"] 4157 }, 4158 "NanoTube": { 4159 "name": "NanoTube", 4160 "version": "1.16.0", 4161 "sha256": "0v4sxb205in1jrr79rvmcw8qp9pa0azb44crl1kmc9kvf9sh0p03", 4162 "depends": ["Biobase", "fgsea", "ggplot2", "limma", "reshape"] 4163 }, 4164 "Nebulosa": { 4165 "name": "Nebulosa", 4166 "version": "1.20.0", 4167 "sha256": "0xb2xj3rj2hqaz1hhsijk83n3qvwp646gj3nx6y8s6k6kda3mwvr", 4168 "depends": ["Matrix", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggrastr", "ks", "patchwork"] 4169 }, 4170 "NetActivity": { 4171 "name": "NetActivity", 4172 "version": "1.12.0", 4173 "sha256": "0ckjlx4ap2k8jk6ji3mg9dkkyqjyk5rw32p4qcpi0ysj0jvz020q", 4174 "depends": ["DESeq2", "DelayedArray", "DelayedMatrixStats", "NetActivityData", "SummarizedExperiment", "airway"] 4175 }, 4176 "NetPathMiner": { 4177 "name": "NetPathMiner", 4178 "version": "1.46.0", 4179 "sha256": "18fvsd8nly7c35370id6ffx0skb82cp78si4qj889sdfgprh1haf", 4180 "depends": ["igraph"] 4181 }, 4182 "NetSAM": { 4183 "name": "NetSAM", 4184 "version": "1.50.0", 4185 "sha256": "19jxwwd3ysd2b4h14rxybhf2m2bfs78szmjs36fqbwxb2ms8h0za", 4186 "depends": ["AnnotationDbi", "DBI", "GO_db", "R2HTML", "WGCNA", "biomaRt", "doParallel", "foreach", "igraph", "seriation", "survival"] 4187 }, 4188 "NewWave": { 4189 "name": "NewWave", 4190 "version": "1.20.0", 4191 "sha256": "07yyj18891kkw5mim6gbc0vzadkafyqazhxrhbqmixr0pa29s7qr", 4192 "depends": ["BiocSingular", "DelayedArray", "Matrix", "SharedObject", "SingleCellExperiment", "SummarizedExperiment", "irlba"] 4193 }, 4194 "NoRCE": { 4195 "name": "NoRCE", 4196 "version": "1.22.0", 4197 "sha256": "1sijrvp5l8bqn4ydklqknfgl1ikdj9lw9yzj3f3pdajgb644dmcc", 4198 "depends": ["AnnotationDbi", "DBI", "GO_db", "GenomicFeatures", "GenomicRanges", "IRanges", "KEGGREST", "RCurl", "RSQLite", "S4Vectors", "Seqinfo", "SummarizedExperiment", "biomaRt", "dbplyr", "dplyr", "ggplot2", "igraph", "png", "rWikiPathways", "reactome_db", "readr", "reshape2", "rtracklayer", "stringr", "tidyr"] 4199 }, 4200 "NormalyzerDE": { 4201 "name": "NormalyzerDE", 4202 "version": "1.28.0", 4203 "sha256": "0xdgkvgh6m607m074kqqm2ajr7hagc0qdhsp2bwqkhr5kryhpdjb", 4204 "depends": ["MASS", "SummarizedExperiment", "ape", "car", "ggforce", "ggplot2", "limma", "matrixStats", "preprocessCore", "vsn"] 4205 }, 4206 "NormqPCR": { 4207 "name": "NormqPCR", 4208 "version": "1.56.0", 4209 "sha256": "002jxkrqbm09xbaaacr3gd50c6pndsgqyfppg0kfyd4grhl3v0p5", 4210 "depends": ["Biobase", "RColorBrewer", "ReadqPCR", "qpcR"] 4211 }, 4212 "NuPoP": { 4213 "name": "NuPoP", 4214 "version": "2.18.0", 4215 "sha256": "0v6fmvv35mhz4w3vdz6rlj13llrzrzgclc7aaa2pqh277cnpvsbv", 4216 "depends": [] 4217 }, 4218 "OCplus": { 4219 "name": "OCplus", 4220 "version": "1.84.0", 4221 "sha256": "1xqlb22qaiqmf73hqzwb8xqimc8nxsi6qr12bbdn8452izx32syv", 4222 "depends": ["interp", "multtest"] 4223 }, 4224 "OGRE": { 4225 "name": "OGRE", 4226 "version": "1.14.0", 4227 "sha256": "1s32r0gjqpg7hkysz83m7i2xm3nxi9nl7pfpdqjlxxpcz0n67gnx", 4228 "depends": ["AnnotationHub", "DT", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "Seqinfo", "assertthat", "data_table", "ggplot2", "rtracklayer", "shiny", "shinyBS", "shinyFiles", "shinydashboard", "tidyr"] 4229 }, 4230 "OLIN": { 4231 "name": "OLIN", 4232 "version": "1.88.0", 4233 "sha256": "1vd4c6y7csfcmlsdgzq7jq1lnp7pffbbppkby0y137jh7lzr1sjf", 4234 "depends": ["limma", "locfit", "marray"] 4235 }, 4236 "OLINgui": { 4237 "name": "OLINgui", 4238 "version": "1.84.0", 4239 "sha256": "1x2lmcgfccqxnf1zpyczkhh8vpw6p6zpp1rqp1048b7mqahpsddw", 4240 "depends": ["OLIN", "marray", "tkWidgets", "widgetTools"] 4241 }, 4242 "OMICsPCA": { 4243 "name": "OMICsPCA", 4244 "version": "1.28.0", 4245 "sha256": "0qnk5ayhmxb99zbmpjp0pnmk6fbx5siqlafvqadinrjpm2nhihqr", 4246 "depends": ["FactoMineR", "HelloRanges", "IRanges", "MASS", "MultiAssayExperiment", "NbClust", "OMICsPCAdata", "PerformanceAnalytics", "Seqinfo", "clValid", "cluster", "corrplot", "cowplot", "data_table", "factoextra", "fpc", "ggplot2", "kableExtra", "magick", "pdftools", "reshape2", "rgl", "rmarkdown", "rtracklayer", "tidyr"] 4247 }, 4248 "OPWeight": { 4249 "name": "OPWeight", 4250 "version": "1.32.0", 4251 "sha256": "14r3v31zddcaa8xbf09v4fs11iwsqjwjqb09hy9v46bgbmgy6bk3", 4252 "depends": ["MASS", "qvalue", "tibble"] 4253 }, 4254 "ORFhunteR": { 4255 "name": "ORFhunteR", 4256 "version": "1.18.0", 4257 "sha256": "00qjdd3lxsjglq9lhaf15q64gprf9dlwdx4p2a5g5qdghb2fpscx", 4258 "depends": ["BSgenome_Hsapiens_UCSC_hg38", "Biostrings", "Peptides", "Rcpp", "data_table", "randomForest", "rtracklayer", "stringr", "xfun"] 4259 }, 4260 "ORFik": { 4261 "name": "ORFik", 4262 "version": "1.30.0", 4263 "sha256": "122ssy6zdibc5zshrizg45l5943g54ahhr8m9x1niz2gfv1639vv", 4264 "depends": ["AnnotationDbi", "BSgenome", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "Rcpp", "Rsamtools", "S4Vectors", "SummarizedExperiment", "XML", "biomaRt", "biomartr", "cowplot", "data_table", "fst", "ggplot2", "gridExtra", "httr", "jsonlite", "qs", "rtracklayer", "txdbmaker", "withr", "xml2"] 4265 }, 4266 "OSAT": { 4267 "name": "OSAT", 4268 "version": "1.58.0", 4269 "sha256": "0k92c8vyjl4cpdiizy5ffq05prwdp6nindxl3w26lnh3m65p59va", 4270 "depends": [] 4271 }, 4272 "OSTA_data": { 4273 "name": "OSTA.data", 4274 "version": "1.1.2", 4275 "sha256": "0bxhjk8vyz1ylni0wkm6pqhdc6g98ak1n1fvcrr5zrm30vf5vfyf", 4276 "depends": ["BiocFileCache", "osfr"] 4277 }, 4278 "OTUbase": { 4279 "name": "OTUbase", 4280 "version": "1.60.0", 4281 "sha256": "1yqzkmfl71i4kk1xy5vgw8rnhjr2xh5zpdr99xirgkhz3xbay27h", 4282 "depends": ["Biobase", "Biostrings", "IRanges", "S4Vectors", "ShortRead", "vegan"] 4283 }, 4284 "OUTRIDER": { 4285 "name": "OUTRIDER", 4286 "version": "1.28.0", 4287 "sha256": "0fgypmzap54d8bmln0y3fb9s2xyiz3v9zigfslwh7bbm8wnrqblx", 4288 "depends": ["BBmisc", "BiocGenerics", "BiocParallel", "DESeq2", "GenomicFeatures", "GenomicRanges", "IRanges", "PRROC", "RColorBrewer", "RMTstat", "Rcpp", "RcppArmadillo", "S4Vectors", "SummarizedExperiment", "data_table", "generics", "ggplot2", "ggrepel", "heatmaply", "matrixStats", "pcaMethods", "pheatmap", "plotly", "plyr", "pracma", "reshape2", "scales", "txdbmaker"] 4289 }, 4290 "OVESEG": { 4291 "name": "OVESEG", 4292 "version": "1.26.0", 4293 "sha256": "0d9cmf9yzqyw6ksf54sv1iyzc6nzzahzr2dj9ghhc9s5hx0p2fhw", 4294 "depends": ["BiocParallel", "Rcpp", "SummarizedExperiment", "fdrtool", "limma"] 4295 }, 4296 "OmaDB": { 4297 "name": "OmaDB", 4298 "version": "2.26.0", 4299 "sha256": "08b4w22inxykx3843a5yflq1iwr1w1ld3yd2bdnbmv23wf98khlm", 4300 "depends": ["Biostrings", "GenomicRanges", "IRanges", "ape", "httr", "jsonlite", "plyr", "topGO"] 4301 }, 4302 "OmicCircos": { 4303 "name": "OmicCircos", 4304 "version": "1.48.0", 4305 "sha256": "0227a1zi1aqnaqz0wrvvya5py6wrcggmlj8px7bc17bimcaa95i4", 4306 "depends": ["GenomicRanges"] 4307 }, 4308 "Omixer": { 4309 "name": "Omixer", 4310 "version": "1.20.0", 4311 "sha256": "1bxyvk26dlbdci5n0k4j3sm1gni4b9w5b5zrv47isd382j406pb2", 4312 "depends": ["dplyr", "forcats", "ggplot2", "gridExtra", "magrittr", "readr", "stringr", "tibble", "tidyselect"] 4313 }, 4314 "OncoScore": { 4315 "name": "OncoScore", 4316 "version": "1.38.0", 4317 "sha256": "1ql4xlzj2cd4pr2j5zzb6xc1zhpp350ff79i9w74g8ir5c548m6a", 4318 "depends": ["biomaRt"] 4319 }, 4320 "OncoSimulR": { 4321 "name": "OncoSimulR", 4322 "version": "4.12.0", 4323 "sha256": "18y9qdp3wzgc9chs89w9di4z34l2a3shzdwp8vga3mcw5h5issnr", 4324 "depends": ["RColorBrewer", "Rcpp", "Rgraphviz", "car", "data_table", "dplyr", "ggplot2", "ggrepel", "graph", "gtools", "igraph", "smatr", "stringr"] 4325 }, 4326 "OpenStats": { 4327 "name": "OpenStats", 4328 "version": "1.22.0", 4329 "sha256": "0j9i3ija2x47gvg3r3nqshcjk1k43g032d851z6mqhg5aqv6kmbs", 4330 "depends": ["AICcmodavg", "Hmisc", "MASS", "car", "jsonlite", "knitr", "nlme", "rlist", "summarytools"] 4331 }, 4332 "OrderedList": { 4333 "name": "OrderedList", 4334 "version": "1.82.0", 4335 "sha256": "10yb9yfpkynzhl9kw93sj3vs87ly3rjgjdzcgj4lyd2fz9n5h3xy", 4336 "depends": ["Biobase", "twilight"] 4337 }, 4338 "Organism_dplyr": { 4339 "name": "Organism.dplyr", 4340 "version": "1.37.1", 4341 "sha256": "0n9qfwx54pniyb849cx5whnf9hbrsiqyd6xn4bqhq4sl29ly3npd", 4342 "depends": ["AnnotationDbi", "AnnotationFilter", "BiocFileCache", "DBI", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "Seqinfo", "dbplyr", "dplyr", "rlang", "tibble"] 4343 }, 4344 "OrganismDbi": { 4345 "name": "OrganismDbi", 4346 "version": "1.52.0", 4347 "sha256": "180d26ri4r9fdzx1fvggif9yy6xgi1ys8zf11llhman65wwl1w6d", 4348 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocManager", "DBI", "GenomicFeatures", "GenomicRanges", "IRanges", "RBGL", "S4Vectors", "Seqinfo", "graph"] 4349 }, 4350 "Oscope": { 4351 "name": "Oscope", 4352 "version": "1.40.0", 4353 "sha256": "1z1ghy7ix9gk613ilwqrmij91qych3slyrwp68vdhclkx5bs917b", 4354 "depends": ["BiocParallel", "EBSeq", "cluster", "testthat"] 4355 }, 4356 "OutSplice": { 4357 "name": "OutSplice", 4358 "version": "1.10.0", 4359 "sha256": "13c7ssnjkyb5fhzr2d47x7c4pqbgacs6rj8965b61jq25g2yscvi", 4360 "depends": ["AnnotationDbi", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "org_Hs_eg_db"] 4361 }, 4362 "PAA": { 4363 "name": "PAA", 4364 "version": "1.44.0", 4365 "sha256": "03rbqcly1gjcflbwxfn3lw1c6rdi96201lx15hq12b88hr6hzxk3", 4366 "depends": ["MASS", "ROCR", "Rcpp", "e1071", "gplots", "gtools", "limma", "mRMRe", "randomForest", "sva"] 4367 }, 4368 "PADOG": { 4369 "name": "PADOG", 4370 "version": "1.52.0", 4371 "sha256": "1l33q9vnmq9dlxdvx0f25zb01ynxi6pw5gwbqcl8fdz6f4b4slan", 4372 "depends": ["AnnotationDbi", "Biobase", "GSA", "KEGGREST", "KEGGdzPathwaysGEO", "doRNG", "foreach", "hgu133a_db", "hgu133plus2_db", "limma", "nlme"] 4373 }, 4374 "PAIRADISE": { 4375 "name": "PAIRADISE", 4376 "version": "1.26.0", 4377 "sha256": "1gmm2p4zgxqmgn90q4cr1qh2wrsazs5ls4jw9w5sps48i98laggd", 4378 "depends": ["BiocParallel", "S4Vectors", "SummarizedExperiment", "abind", "nloptr"] 4379 }, 4380 "PANR": { 4381 "name": "PANR", 4382 "version": "1.56.0", 4383 "sha256": "0w4gxxhic91zdw0gh4hzy4sbpdfqvxy8m1riga2qy1sy2zh7wgkx", 4384 "depends": ["MASS", "RedeR", "igraph", "pvclust"] 4385 }, 4386 "PAST": { 4387 "name": "PAST", 4388 "version": "1.26.0", 4389 "sha256": "0kyh078cphc27djbk76mdgd6mz0zwnbx0rmvsp0nrm0vj8y6zflq", 4390 "depends": ["GenomicRanges", "S4Vectors", "doParallel", "dplyr", "foreach", "ggplot2", "iterators", "qvalue", "rlang", "rtracklayer"] 4391 }, 4392 "PCAN": { 4393 "name": "PCAN", 4394 "version": "1.38.0", 4395 "sha256": "15bcrr5mij4zvj2m195i4spvz8bp4rffd9154x4zf18k7m50vrrv", 4396 "depends": ["BiocParallel"] 4397 }, 4398 "PDATK": { 4399 "name": "PDATK", 4400 "version": "1.18.0", 4401 "sha256": "0awhbxqp8kmjak7lffkwvhqdk4bgpgs15kc2icyfzbk7hm1l8lg7", 4402 "depends": ["BiocGenerics", "BiocParallel", "ConsensusClusterPlus", "CoreGx", "MatrixGenerics", "MultiAssayExperiment", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "caret", "clusterRepro", "data_table", "dplyr", "genefu", "ggplot2", "ggplotify", "igraph", "matrixStats", "pROC", "piano", "plyr", "reportROC", "rlang", "scales", "survcomp", "survival", "survminer", "switchBox", "verification"] 4403 }, 4404 "PECA": { 4405 "name": "PECA", 4406 "version": "1.46.0", 4407 "sha256": "03bjxl5kx42090zsnbfanqjr09rj21h6m21alys7d1qr1h2mi7p0", 4408 "depends": ["ROTS", "affy", "aroma_affymetrix", "aroma_core", "genefilter", "limma", "preprocessCore"] 4409 }, 4410 "PICB": { 4411 "name": "PICB", 4412 "version": "1.2.0", 4413 "sha256": "1wzf3d3x7c01cbqmy42m0nkhg93ff2k5dpj3air73dpdkif0wh1n", 4414 "depends": ["Biostrings", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "data_table", "dplyr", "openxlsx", "seqinr"] 4415 }, 4416 "PIPETS": { 4417 "name": "PIPETS", 4418 "version": "1.6.0", 4419 "sha256": "1nrfwhlzw4ygfgc6bv75xahj70q5cx314i78gapvmx6z3m63j9f1", 4420 "depends": ["BiocGenerics", "GenomicRanges", "dplyr"] 4421 }, 4422 "PIUMA": { 4423 "name": "PIUMA", 4424 "version": "1.5.0", 4425 "sha256": "1k2gv9m1wcsc3awcbhmcmw0n8jh2grpzkagdj3gvqmvxli7ds2zi", 4426 "depends": ["Hmisc", "SummarizedExperiment", "cluster", "dbscan", "ggplot2", "igraph", "kernlab", "patchwork", "scales", "tsne", "umap", "vegan"] 4427 }, 4428 "PLPE": { 4429 "name": "PLPE", 4430 "version": "1.70.0", 4431 "sha256": "0kyh0vpg1gmj0yriasp8algnmg0yn0ar7aqcssri3752bcv9g6fx", 4432 "depends": ["Biobase", "LPE", "MASS"] 4433 }, 4434 "PLSDAbatch": { 4435 "name": "PLSDAbatch", 4436 "version": "1.6.0", 4437 "sha256": "0fvmpdmldd9f5kza9x5lnkrx9r445sndpdrh4xj49lflbzxlzn5s", 4438 "depends": ["Biobase", "BiocStyle", "Rdpack", "TreeSummarizedExperiment", "ggplot2", "ggpubr", "gridExtra", "lmerTest", "mixOmics", "performance", "pheatmap", "scales", "vegan"] 4439 }, 4440 "PMScanR": { 4441 "name": "PMScanR", 4442 "version": "1.0.0", 4443 "sha256": "15qmll6nirl8whq4r1g13h7xycm5lmzq4rlqh291kw13fyy80acm", 4444 "depends": ["BiocFileCache", "bslib", "dplyr", "ggplot2", "ggseqlogo", "magrittr", "plotly", "reshape2", "rlang", "rtracklayer", "seqinr", "shiny", "shinyFiles", "stringr"] 4445 }, 4446 "POMA": { 4447 "name": "POMA", 4448 "version": "1.20.0", 4449 "sha256": "11z36bzsch3j2b1pnifkjpyb0m1a5aq2l7k69icwj4ihbj8hv6ba", 4450 "depends": ["ComplexHeatmap", "DESeq2", "FSA", "MASS", "RankProd", "SummarizedExperiment", "broom", "caret", "dbscan", "dplyr", "fgsea", "ggcorrplot", "ggplot2", "ggrepel", "glmnet", "impute", "janitor", "limma", "lme4", "magrittr", "mixOmics", "msigdbr", "multcomp", "purrr", "randomForest", "rlang", "sva", "tibble", "tidyr", "uwot", "vegan"] 4451 }, 4452 "POWSC": { 4453 "name": "POWSC", 4454 "version": "1.18.0", 4455 "sha256": "1sk5sk51k7cyq2yh5x4fygsgibdm2vqv8nnwfp96328x1nlf1kak", 4456 "depends": ["Biobase", "MAST", "RColorBrewer", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "limma", "pheatmap"] 4457 }, 4458 "PPInfer": { 4459 "name": "PPInfer", 4460 "version": "1.36.0", 4461 "sha256": "02hwar7xg1l2qd035pvdzmy6hlsdqxllrps8xd7dd9bcyc3nnq4g", 4462 "depends": ["STRINGdb", "biomaRt", "fgsea", "ggplot2", "httr", "igraph", "kernlab", "yeastExpData"] 4463 }, 4464 "PREDA": { 4465 "name": "PREDA", 4466 "version": "1.56.0", 4467 "sha256": "1yi4hs4hwp1pwf8rivjqkfcrgzixfmiqdl8raf38la683andq2m1", 4468 "depends": ["Biobase", "annotate", "lokern", "multtest"] 4469 }, 4470 "PROMISE": { 4471 "name": "PROMISE", 4472 "version": "1.62.0", 4473 "sha256": "1daz6g1awdsb2yxfb390341yx8zl4xrilgdai6h2ci0qd4wffrz2", 4474 "depends": ["Biobase", "GSEABase"] 4475 }, 4476 "PRONE": { 4477 "name": "PRONE", 4478 "version": "1.4.0", 4479 "sha256": "18l7f0mbs3gr1kasx81b6yayiqh06w7n1wcb4s68yw8q0cj4giv3", 4480 "depends": ["Biobase", "ComplexHeatmap", "ComplexUpset", "DEqMS", "MASS", "MSnbase", "NormalyzerDE", "POMA", "RColorBrewer", "ROTS", "S4Vectors", "SummarizedExperiment", "UpSetR", "circlize", "data_table", "dendsort", "dplyr", "edgeR", "ggplot2", "ggtext", "gprofiler2", "gtools", "limma", "magrittr", "matrixStats", "plotROC", "preprocessCore", "purrr", "reshape2", "scales", "stringr", "tibble", "tidyr", "vegan", "vsn"] 4481 }, 4482 "PROPER": { 4483 "name": "PROPER", 4484 "version": "1.42.0", 4485 "sha256": "1a93nn3p9s09ncaddif07nwq9xwmfx85c11chap1yb398f19czj5", 4486 "depends": ["edgeR"] 4487 }, 4488 "PROPS": { 4489 "name": "PROPS", 4490 "version": "1.32.0", 4491 "sha256": "0wlsavvln63sljmyf220xvs7rndqqylmnlrpwqpzffb3jw7djqjs", 4492 "depends": ["Biobase", "bnlearn", "reshape2", "sva"] 4493 }, 4494 "PROcess": { 4495 "name": "PROcess", 4496 "version": "1.86.0", 4497 "sha256": "0hjcpmx0kx64fy1hlji0dbqr4d8r65v17z8a1lwh83ggn83mwz6a", 4498 "depends": ["Icens"] 4499 }, 4500 "PSMatch": { 4501 "name": "PSMatch", 4502 "version": "1.14.0", 4503 "sha256": "021axxxc4590m350mcs14glyygzsy4m7x6zg3isfxn1rhsva351r", 4504 "depends": ["BiocGenerics", "BiocParallel", "IRanges", "Matrix", "MsCoreUtils", "ProtGenerics", "QFeatures", "S4Vectors", "Spectra", "igraph"] 4505 }, 4506 "PWMEnrich": { 4507 "name": "PWMEnrich", 4508 "version": "4.46.0", 4509 "sha256": "07kcd91ziq0bf76q3437vr4rpvllx5f8bm6mbqndgbxffz4ar9q5", 4510 "depends": ["BiocGenerics", "Biostrings", "S4Vectors", "evd", "gdata", "seqLogo"] 4511 }, 4512 "PanomiR": { 4513 "name": "PanomiR", 4514 "version": "1.14.0", 4515 "sha256": "0w9jm6xfrp42rwblq9b1xc17bqybv8m9b4sc44bbir5jb3x3cffi", 4516 "depends": ["GSEABase", "RColorBrewer", "clusterProfiler", "dplyr", "forcats", "igraph", "limma", "metap", "org_Hs_eg_db", "preprocessCore", "rlang", "tibble", "withr"] 4517 }, 4518 "Path2PPI": { 4519 "name": "Path2PPI", 4520 "version": "1.40.0", 4521 "sha256": "10ziydlb83piccczmygq2s8vlrnbi7kksz8f5zc46myg8cz0lpdc", 4522 "depends": ["igraph"] 4523 }, 4524 "PathNet": { 4525 "name": "PathNet", 4526 "version": "1.50.0", 4527 "sha256": "0jbvw17acxmv3hcfjzkhgfdc24qvfm5w8a5pda8gqyahjm2vnhvq", 4528 "depends": [] 4529 }, 4530 "PathoStat": { 4531 "name": "PathoStat", 4532 "version": "1.36.0", 4533 "sha256": "12l79rj60iibn9vgvsjwnsnsprba6i507q3852gdagamvfziar57", 4534 "depends": ["BiocStyle", "ComplexHeatmap", "DESeq2", "DT", "RColorBrewer", "ROCR", "XML", "ape", "corpcor", "devtools", "dplyr", "edgeR", "ggplot2", "glmnet", "gmodels", "knitr", "limma", "matrixStats", "phyloseq", "plotly", "plyr", "rentrez", "reshape2", "scales", "shiny", "shinyjs", "tidyr", "vegan", "webshot"] 4535 }, 4536 "PeacoQC": { 4537 "name": "PeacoQC", 4538 "version": "1.20.0", 4539 "sha256": "05pv91clpdb6mq1ki8zp67rd7l414g7nacxcgqpxvdxwf35byibg", 4540 "depends": ["ComplexHeatmap", "circlize", "flowCore", "flowWorkspace", "ggplot2", "gridExtra", "plyr"] 4541 }, 4542 "Pedixplorer": { 4543 "name": "Pedixplorer", 4544 "version": "1.6.0", 4545 "sha256": "0yih17g5950ykrflyhlgwdhjlb23wcm5xsf3901za5dm1nxak0ag", 4546 "depends": ["DT", "Matrix", "S4Vectors", "colourpicker", "dplyr", "ggplot2", "htmlwidgets", "igraph", "plotly", "plyr", "quadprog", "readxl", "shiny", "shinyWidgets", "shinycssloaders", "shinyhelper", "shinyjqui", "shinyjs", "shinytoastr", "stringr", "tidyr"] 4547 }, 4548 "PepSetTest": { 4549 "name": "PepSetTest", 4550 "version": "1.4.0", 4551 "sha256": "0f60csg07bbsf5jjpzrxr8sdrr35q889990iaxbp7l9g0im0aygg", 4552 "depends": ["MASS", "SummarizedExperiment", "dplyr", "limma", "lme4", "matrixStats", "reshape2", "tibble"] 4553 }, 4554 "PepsNMR": { 4555 "name": "PepsNMR", 4556 "version": "1.28.0", 4557 "sha256": "16fmlwhwgyw703n6m7f5r3y2kh3ix7qzblzcw1ckaxc0sak3p8fg", 4558 "depends": ["Matrix", "ggplot2", "gridExtra", "matrixStats", "ptw", "reshape2"] 4559 }, 4560 "PhIPData": { 4561 "name": "PhIPData", 4562 "version": "1.18.0", 4563 "sha256": "0lj06ym0414hqxi1i6k7xbjrh7clhmw30gam39f34kf28iw8cc52", 4564 "depends": ["BiocFileCache", "BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "cli", "edgeR"] 4565 }, 4566 "PharmacoGx": { 4567 "name": "PharmacoGx", 4568 "version": "3.14.0", 4569 "sha256": "1hz9cqhxsi13icw6my1yamx97nqcj684jgjxpfrh88qlq0diq04h", 4570 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "CoreGx", "MultiAssayExperiment", "RColorBrewer", "Rcpp", "S4Vectors", "SummarizedExperiment", "boot", "caTools", "checkmate", "coop", "data_table", "downloader", "ggplot2", "jsonlite", "magicaxis", "reshape2"] 4571 }, 4572 "PhenoGeneRanker": { 4573 "name": "PhenoGeneRanker", 4574 "version": "1.18.0", 4575 "sha256": "1c9bjzn6f3j3bl1z4wfcyx21pwh2hrqpj3ack4b4h5hbmr0r8ilr", 4576 "depends": ["Matrix", "doParallel", "dplyr", "foreach", "igraph"] 4577 }, 4578 "PhosR": { 4579 "name": "PhosR", 4580 "version": "1.20.0", 4581 "sha256": "0m7nxwnsanwwxd6yhc07hw96qm8p7bkyafn41p66g5zkaq2xrfwz", 4582 "depends": ["BiocGenerics", "GGally", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "circlize", "dendextend", "dplyr", "e1071", "ggdendro", "ggplot2", "ggpubr", "ggtext", "igraph", "limma", "network", "pcaMethods", "pheatmap", "preprocessCore", "reshape2", "rlang", "ruv", "stringi", "tidyr"] 4583 }, 4584 "PhyloProfile": { 4585 "name": "PhyloProfile", 4586 "version": "2.2.0", 4587 "sha256": "1rmq0x7gc0l6h585qywlf6gsk3l72p7qqzlg0dmwwv7v9h5mdmv8", 4588 "depends": ["BiocStyle", "Biostrings", "DT", "RColorBrewer", "RCurl", "Rfast", "ape", "bioDist", "bsplus", "colourpicker", "data_table", "dplyr", "energy", "fastcluster", "ggplot2", "gridExtra", "htmlwidgets", "pbapply", "plotly", "scattermore", "shiny", "shinyFiles", "shinycssloaders", "shinyjs", "stringr", "svglite", "tsne", "umap", "xml2", "yaml", "zoo"] 4589 }, 4590 "PoDCall": { 4591 "name": "PoDCall", 4592 "version": "1.18.0", 4593 "sha256": "07aa8d1zxgm4nqs86maj6h2xmfyg6bicwyflab8fr2glq89ssjap", 4594 "depends": ["DT", "LaplacesDemon", "diptest", "ggplot2", "gridExtra", "mclust", "purrr", "readr", "rlist", "shiny", "shinyjs"] 4595 }, 4596 "PolySTest": { 4597 "name": "PolySTest", 4598 "version": "1.4.0", 4599 "sha256": "00zq59qj0hv956sfh93vwbdqiv77909b7zl114kjm2gvgrcpwfqm", 4600 "depends": ["S4Vectors", "SummarizedExperiment", "UpSetR", "circlize", "fdrtool", "gplots", "heatmaply", "knitr", "limma", "matrixStats", "plotly", "qvalue", "shiny"] 4601 }, 4602 "Polytect": { 4603 "name": "Polytect", 4604 "version": "1.2.0", 4605 "sha256": "0a3myqbiqqnd669azx3qk9szc37436kffkd7gvy4kr3q8qaz4v4n", 4606 "depends": ["BiocManager", "DiceKriging", "ParamHelpers", "cowplot", "dplyr", "flowPeaks", "ggplot2", "lhs", "mlrMBO", "mvtnorm", "rgenoud", "smoof", "sn", "tidyverse"] 4607 }, 4608 "PrInCE": { 4609 "name": "PrInCE", 4610 "version": "1.26.0", 4611 "sha256": "0c0jvjjc8syf2g6rj58475nxfa3h1qrc45iv36qzs1mwpdx5j5rw", 4612 "depends": ["Biobase", "Hmisc", "LiblineaR", "MSnbase", "Rdpack", "dplyr", "forecast", "magrittr", "naivebayes", "progress", "purrr", "ranger", "robustbase", "speedglm", "tester", "tidyr"] 4613 }, 4614 "Prostar": { 4615 "name": "Prostar", 4616 "version": "1.42.0", 4617 "sha256": "1dg838si4bcs5i29q7yhsj5g2cdvddnqc19zqmf5gxpvj84l7r9l", 4618 "depends": ["Biobase", "DAPAR", "DAPARdata", "DT", "RColorBrewer", "R_utils", "XML", "colourpicker", "data_table", "future", "ggplot2", "gplots", "gtools", "highcharter", "htmlwidgets", "later", "markdown", "promises", "rclipboard", "rhandsontable", "sass", "shiny", "shinyAce", "shinyBS", "shinyTree", "shinyWidgets", "shinycssloaders", "shinyjqui", "shinyjs", "shinythemes", "tibble", "vioplot", "webshot"] 4619 }, 4620 "ProtGenerics": { 4621 "name": "ProtGenerics", 4622 "version": "1.42.0", 4623 "sha256": "0g9d54az95qvqqnsbqjr4001jzfpwzs4apfjywxaha4k8cavb69f", 4624 "depends": [] 4625 }, 4626 "ProteoDisco": { 4627 "name": "ProteoDisco", 4628 "version": "1.16.0", 4629 "sha256": "13d46s2vzpkxq423cwhd26zhgxib28jh7dcmkm2pz704qgd988s8", 4630 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "ParallelLogger", "S4Vectors", "Seqinfo", "VariantAnnotation", "XVector", "checkmate", "cleaver", "dplyr", "plyr", "rlang", "tibble", "tidyr"] 4631 }, 4632 "ProteoMM": { 4633 "name": "ProteoMM", 4634 "version": "1.28.0", 4635 "sha256": "1swqzig7dlkqq4kr8pbhfh3q2lk4c5cbm3knx14y86xpx9xsgqik", 4636 "depends": ["biomaRt", "gdata", "ggplot2", "ggrepel", "gtools", "matrixStats"] 4637 }, 4638 "PureCN": { 4639 "name": "PureCN", 4640 "version": "2.16.0", 4641 "sha256": "1kzp4avvnzih12m7c46n440msrrb97ibsjzwf6ay1l7n8qrjmqqi", 4642 "depends": ["Biobase", "BiocGenerics", "Biostrings", "DNAcopy", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VGAM", "VariantAnnotation", "data_table", "futile_logger", "ggplot2", "gridExtra", "mclust", "rhdf5", "rtracklayer"] 4643 }, 4644 "Pviz": { 4645 "name": "Pviz", 4646 "version": "1.44.0", 4647 "sha256": "196x9n0rs1cs9c2j11fg8a2w09rpbmzgm6pwmamc8mqir91yajzk", 4648 "depends": ["Biostrings", "GenomicRanges", "Gviz", "IRanges", "biovizBase", "data_table"] 4649 }, 4650 "QDNAseq": { 4651 "name": "QDNAseq", 4652 "version": "1.46.0", 4653 "sha256": "12bf7x4c2vhq28vbzj322yp2gyvwcakpw13x6bsi3r87vg8rfdlr", 4654 "depends": ["Biobase", "BiocGenerics", "CGHbase", "CGHcall", "DNAcopy", "GenomicRanges", "IRanges", "R_utils", "Rsamtools", "Seqinfo", "future_apply", "matrixStats"] 4655 }, 4656 "QFeatures": { 4657 "name": "QFeatures", 4658 "version": "1.20.0", 4659 "sha256": "0q14b2ppvdd9gb89xp86gdn45krzv5sz1n3f6ip6qxi8nn293lzy", 4660 "depends": ["AnnotationFilter", "Biobase", "BiocGenerics", "IRanges", "MsCoreUtils", "MultiAssayExperiment", "ProtGenerics", "S4Vectors", "SummarizedExperiment", "igraph", "lazyeval", "plotly", "reshape2", "tidyr", "tidyselect"] 4661 }, 4662 "QRscore": { 4663 "name": "QRscore", 4664 "version": "1.2.0", 4665 "sha256": "1wh503rrfghah7xk3dj7rxxajg8s0xfyj6xczz4a007bc93hv976", 4666 "depends": ["BiocParallel", "MASS", "arrangements", "assertthat", "dplyr", "hitandrun", "pscl"] 4667 }, 4668 "QSutils": { 4669 "name": "QSutils", 4670 "version": "1.28.0", 4671 "sha256": "04f0jslf8cg93yz14nhf9rqpnaslbyg6vnlspjs2rf6lpdjqjx34", 4672 "depends": ["BiocGenerics", "Biostrings", "ape", "psych", "pwalign"] 4673 }, 4674 "QTLExperiment": { 4675 "name": "QTLExperiment", 4676 "version": "2.2.0", 4677 "sha256": "1dx94w8kjdn2vs8kyvdwik7hjgi5rv2ixmgjjck9ri5lh7488nhi", 4678 "depends": ["BiocGenerics", "S4Vectors", "SummarizedExperiment", "ashr", "checkmate", "collapse", "dplyr", "rlang", "tibble", "tidyr", "vroom"] 4679 }, 4680 "QUBIC": { 4681 "name": "QUBIC", 4682 "version": "1.38.0", 4683 "sha256": "1x3kps3n6qqkdm5q3c0mhy10d2f9a059afqc84n6vqcdvh9zbhsj", 4684 "depends": ["Matrix", "Rcpp", "RcppArmadillo", "biclust"] 4685 }, 4686 "Qtlizer": { 4687 "name": "Qtlizer", 4688 "version": "1.24.0", 4689 "sha256": "1fj2lbzn7myxa287b014jyjjfh47qa9x22bqrxvipg1q36kg6xf2", 4690 "depends": ["GenomicRanges", "curl", "httr", "stringi"] 4691 }, 4692 "QuasR": { 4693 "name": "QuasR", 4694 "version": "1.50.0", 4695 "sha256": "145wzdnhjhi0ys8nlsasjqw57f693yf2iichd9045s52x5zjny4h", 4696 "depends": ["AnnotationDbi", "BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "IRanges", "Rbowtie", "Rhtslib", "Rsamtools", "S4Vectors", "Seqinfo", "ShortRead", "rtracklayer", "txdbmaker"] 4697 }, 4698 "QuaternaryProd": { 4699 "name": "QuaternaryProd", 4700 "version": "1.44.0", 4701 "sha256": "1qsjs49byidzd67izzcakf4dvxzgsw7i79ly237ppr8h75nbzc6w", 4702 "depends": ["Rcpp", "dplyr", "yaml"] 4703 }, 4704 "R3CPET": { 4705 "name": "R3CPET", 4706 "version": "1.42.0", 4707 "sha256": "1lj391k0sx58n2rjniixr3l0hkdw2y1hsf492fhj7cnhzph6bdj9", 4708 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "Hmisc", "IRanges", "RCurl", "Rcpp", "S4Vectors", "clValid", "data_table", "ggbio", "ggplot2", "igraph", "pheatmap", "reshape2"] 4709 }, 4710 "R4RNA": { 4711 "name": "R4RNA", 4712 "version": "1.38.0", 4713 "sha256": "1hgyqqw7abkkx525j0i9qhrs0bir29xsxbzg0lg93swfsf4jwily", 4714 "depends": ["Biostrings"] 4715 }, 4716 "RAIDS": { 4717 "name": "RAIDS", 4718 "version": "1.8.0", 4719 "sha256": "150fiaw8nl8b3687aay30n2d36z9310wjhfikglc0l90k4y1a0i8", 4720 "depends": ["AnnotationDbi", "AnnotationFilter", "BSgenome", "GENESIS", "GenomicRanges", "IRanges", "MatrixGenerics", "Rsamtools", "S4Vectors", "SNPRelate", "VariantAnnotation", "class", "dplyr", "ensembldb", "gdsfmt", "ggplot2", "pROC", "rlang", "stringr"] 4721 }, 4722 "RAREsim": { 4723 "name": "RAREsim", 4724 "version": "1.14.0", 4725 "sha256": "0acrjn0zrvi1an8jpjhmlgg6ndnxyd427xvqynq5y4rrl49kh80f", 4726 "depends": ["nloptr"] 4727 }, 4728 "RBGL": { 4729 "name": "RBGL", 4730 "version": "1.86.0", 4731 "sha256": "083gm7biwq5z0jibr3wbdkjs50kqphwjkh571awk8rhlniqwpi1f", 4732 "depends": ["BH", "graph"] 4733 }, 4734 "RBM": { 4735 "name": "RBM", 4736 "version": "1.42.0", 4737 "sha256": "1yqq95503l1jhlppqgirgrrzskhw0h2zap5vrym7ba9x7f42pdcy", 4738 "depends": ["limma", "marray"] 4739 }, 4740 "RBioFormats": { 4741 "name": "RBioFormats", 4742 "version": "1.10.0", 4743 "sha256": "0k1cmh3qdiw2kyidzgn2vbsmnp6ag1nw9v9cr58m5j4hlx5zj2n1", 4744 "depends": ["EBImage", "S4Vectors", "rJava"] 4745 }, 4746 "RCAS": { 4747 "name": "RCAS", 4748 "version": "1.36.0", 4749 "sha256": "1jrwmggylbgq9k7y9b8l176pk5b2r2ggcs2psf2bl2p96wczj4jb", 4750 "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "Biostrings", "DT", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "cowplot", "data_table", "genomation", "ggplot2", "gprofiler2", "knitr", "pbapply", "pheatmap", "plotly", "plotrix", "proxy", "ranger", "rmarkdown", "rtracklayer", "seqLogo", "txdbmaker"] 4751 }, 4752 "RCASPAR": { 4753 "name": "RCASPAR", 4754 "version": "1.56.0", 4755 "sha256": "0076zajkxmmqgwpkw0spfyqx5r5y0nqpqr6jh2yma24wxprhx228", 4756 "depends": [] 4757 }, 4758 "RCM": { 4759 "name": "RCM", 4760 "version": "1.26.0", 4761 "sha256": "1r26gqkzqxv6a8q3a7rdisggznx51v1hn6wq35300wxixzh6nz36", 4762 "depends": ["MASS", "RColorBrewer", "VGAM", "alabama", "edgeR", "ggplot2", "nleqslv", "phyloseq", "reshape2", "tensor", "tseries"] 4763 }, 4764 "RCSL": { 4765 "name": "RCSL", 4766 "version": "1.18.0", 4767 "sha256": "1cq8xzn109knhgzvzvdq8pz677jq5k7zmzn009h1nm9g8vn9fsq6", 4768 "depends": ["MatrixGenerics", "NbClust", "Rcpp", "RcppAnnoy", "Rtsne", "SingleCellExperiment", "ggplot2", "igraph", "pracma", "umap"] 4769 }, 4770 "RCX": { 4771 "name": "RCX", 4772 "version": "1.14.0", 4773 "sha256": "0h7blsgi60na56xgy2m47irqd9ql6dfmifrk1kcgnydcz5wjzr3g", 4774 "depends": ["igraph", "jsonlite", "plyr"] 4775 }, 4776 "RCy3": { 4777 "name": "RCy3", 4778 "version": "2.30.0", 4779 "sha256": "1xc19lvdz6yyg2844j83idv64adfrw1bkpiazd4w39xa46l46lck", 4780 "depends": ["BiocGenerics", "IRdisplay", "IRkernel", "RColorBrewer", "RCurl", "RJSONIO", "XML", "base64enc", "base64url", "fs", "glue", "gplots", "graph", "httr", "stringi", "uuid"] 4781 }, 4782 "RCyjs": { 4783 "name": "RCyjs", 4784 "version": "2.32.0", 4785 "sha256": "0xdflz3m2nrw6w05mmsqpdk5jhzikkfn9wq5fwclhgmr8jr687fm", 4786 "depends": ["BiocGenerics", "BrowserViz", "base64enc", "graph", "httpuv"] 4787 }, 4788 "RDRToolbox": { 4789 "name": "RDRToolbox", 4790 "version": "1.60.0", 4791 "sha256": "1vwbwli7ypchkjr6m5siv9zvy18689fvsnh99w6h9rlisbrhlw7c", 4792 "depends": ["MASS", "rgl"] 4793 }, 4794 "REBET": { 4795 "name": "REBET", 4796 "version": "1.28.0", 4797 "sha256": "17s6rhqvvngx5k39kjw5p1j9wzv8ycak0qlhgqqjchhx2sdk2xrz", 4798 "depends": ["ASSET"] 4799 }, 4800 "REDseq": { 4801 "name": "REDseq", 4802 "version": "1.56.0", 4803 "sha256": "0p0gwhq95s32d7nps5sg7zx0xi7ndg26bzb6yaxx3ymc8qsnpwvv", 4804 "depends": ["AnnotationDbi", "BSgenome", "BSgenome_Celegans_UCSC_ce2", "BiocGenerics", "Biostrings", "ChIPpeakAnno", "IRanges", "multtest"] 4805 }, 4806 "REMP": { 4807 "name": "REMP", 4808 "version": "1.34.0", 4809 "sha256": "1xvzxgcjy1va1spd0g0zfnaa7n2fk0ji3lxki8n7s2qs2r7qpjc5", 4810 "depends": ["AnnotationHub", "BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "SummarizedExperiment", "caret", "doParallel", "foreach", "impute", "iterators", "kernlab", "minfi", "org_Hs_eg_db", "ranger", "readr", "rtracklayer", "settings"] 4811 }, 4812 "RESOLVE": { 4813 "name": "RESOLVE", 4814 "version": "1.12.0", 4815 "sha256": "1r34ahcnbnxaz54zzyl8v3mawl5pbzrn7r43qj9nma1vxklf1yxk", 4816 "depends": ["BSgenome", "BSgenome_Hsapiens_1000genomes_hs37d5", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "MutationalPatterns", "RhpcBLASctl", "S4Vectors", "cluster", "data_table", "ggplot2", "glmnet", "gridExtra", "lsa", "nnls", "reshape2", "survival"] 4817 }, 4818 "RFLOMICS": { 4819 "name": "RFLOMICS", 4820 "version": "1.2.0", 4821 "sha256": "17vjzydinij9sqj2ng6s2hjhb2652rsnzppalfrydf61kdjrk99g", 4822 "depends": ["AnnotationDbi", "ComplexHeatmap", "DT", "FactoMineR", "MOFA2", "MultiAssayExperiment", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "UpSetR", "clusterProfiler", "coseq", "data_table", "dplyr", "edgeR", "enrichplot", "ggplot2", "ggpubr", "ggrepel", "htmltools", "httr", "knitr", "limma", "magrittr", "mixOmics", "org_At_tair_db", "plotly", "purrr", "reshape2", "reticulate", "rmarkdown", "shiny", "shinyBS", "shinyWidgets", "shinydashboard", "stringr", "tibble", "tidyr", "tidyselect", "vroom"] 4823 }, 4824 "RGSEA": { 4825 "name": "RGSEA", 4826 "version": "1.44.0", 4827 "sha256": "1rlx525m2p82fsy4crwsiph6wds8aaqs1nmiyq8r47j0qzkxcblg", 4828 "depends": ["BiocGenerics"] 4829 }, 4830 "RGraph2js": { 4831 "name": "RGraph2js", 4832 "version": "1.38.0", 4833 "sha256": "14j90xk3h20wsrpxq0wacrbnl8vwr6r80fdq415rpaahzg3simhy", 4834 "depends": ["digest", "graph", "rjson", "whisker"] 4835 }, 4836 "RITAN": { 4837 "name": "RITAN", 4838 "version": "1.34.0", 4839 "sha256": "0mj8dvqwvjgyj8igwmyr70rs8244id81q7r7h75ncky8kq74q6kp", 4840 "depends": ["AnnotationFilter", "BgeeDB", "EnsDb_Hsapiens_v86", "GenomicFeatures", "MCL", "RColorBrewer", "RITANdata", "STRINGdb", "dynamicTreeCut", "ensembldb", "ggplot2", "gplots", "gridExtra", "gsubfn", "hash", "igraph", "knitr", "plotrix", "png", "reshape2", "sqldf"] 4841 }, 4842 "RIVER": { 4843 "name": "RIVER", 4844 "version": "1.34.0", 4845 "sha256": "1nf56wlh5v678w6bjgyqkalk7vhimyl6830v64iwfm5mxqj18726", 4846 "depends": ["Biobase", "ggplot2", "glmnet", "pROC"] 4847 }, 4848 "RImmPort": { 4849 "name": "RImmPort", 4850 "version": "1.38.0", 4851 "sha256": "0wljrymp15b7lav18cwfhzfx9m18sk80jaqb0ng53dajz5pvhpyj", 4852 "depends": ["DBI", "RSQLite", "data_table", "dplyr", "plyr", "reshape2", "sqldf"] 4853 }, 4854 "RJMCMCNucleosomes": { 4855 "name": "RJMCMCNucleosomes", 4856 "version": "1.34.0", 4857 "sha256": "17jykk7mffdw5w2rn2bghkmx9yk8vj90vs31xyjhvpfj67n8d1cr", 4858 "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors", "Seqinfo", "consensusSeekeR"] 4859 }, 4860 "RLMM": { 4861 "name": "RLMM", 4862 "version": "1.72.0", 4863 "sha256": "07a4nhwrk697h4k0asb6k53wykhqzgpr07nhzkg4ipy5jcr4yj69", 4864 "depends": ["MASS"] 4865 }, 4866 "RLassoCox": { 4867 "name": "RLassoCox", 4868 "version": "1.18.0", 4869 "sha256": "1393fi1brfnbd1ygqw3ypfrfsv6nspz4fclvqr82pyvlj7wbrlfz", 4870 "depends": ["Matrix", "glmnet", "igraph", "survival"] 4871 }, 4872 "RMassBank": { 4873 "name": "RMassBank", 4874 "version": "3.20.0", 4875 "sha256": "040fzq6gia3922lxgc8w7bnszyyr1yavpca1bzz7jq6rsi2rf2x6", 4876 "depends": ["Biobase", "ChemmineR", "MSnbase", "R_utils", "Rcpp", "S4Vectors", "XML", "assertthat", "data_table", "digest", "dplyr", "enviPat", "glue", "httr", "httr2", "logger", "mzR", "purrr", "rcdk", "readJDX", "readr", "rjson", "tibble", "tidyselect", "webchem", "yaml"] 4877 }, 4878 "RNAAgeCalc": { 4879 "name": "RNAAgeCalc", 4880 "version": "1.22.0", 4881 "sha256": "0fqyiqpwn89ci15q3drvhfgwciiqmc1x82byrjvvjks9h1vmpsb2", 4882 "depends": ["AnnotationDbi", "SummarizedExperiment", "ggplot2", "impute", "org_Hs_eg_db", "recount"] 4883 }, 4884 "RNASeqPower": { 4885 "name": "RNASeqPower", 4886 "version": "1.50.0", 4887 "sha256": "1gv85ngbfmkb0xpx0h27yn6lybxynp3gd3nl18qdjcf4bzs4kx9h", 4888 "depends": [] 4889 }, 4890 "RNAmodR": { 4891 "name": "RNAmodR", 4892 "version": "1.24.0", 4893 "sha256": "0jlvsyyb3pasq72va9imgmsmgwlvngv9d79890gx40rwm8n853cv", 4894 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Modstrings", "RColorBrewer", "ROCR", "Rsamtools", "S4Vectors", "Seqinfo", "colorRamps", "ggplot2", "matrixStats", "reshape2", "rtracklayer", "txdbmaker"] 4895 }, 4896 "RNAmodR_AlkAnilineSeq": { 4897 "name": "RNAmodR.AlkAnilineSeq", 4898 "version": "1.24.0", 4899 "sha256": "1m5nzviikbi6jx6pjzfpg48qxpy4synn22kipyfbxi23cnh6f2zw", 4900 "depends": ["BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "RNAmodR", "S4Vectors"] 4901 }, 4902 "RNAmodR_ML": { 4903 "name": "RNAmodR.ML", 4904 "version": "1.24.0", 4905 "sha256": "04xndcmilalhk27c41a0h7s8whn2v48x7968w6mw8g1g5d3v87jj", 4906 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "RNAmodR", "S4Vectors", "ranger"] 4907 }, 4908 "RNAmodR_RiboMethSeq": { 4909 "name": "RNAmodR.RiboMethSeq", 4910 "version": "1.24.0", 4911 "sha256": "0wnayl13fpiy94zn6mn6k2rj9fc1v8iayb2hcarq1zqb06q0jgbp", 4912 "depends": ["BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "RNAmodR", "S4Vectors"] 4913 }, 4914 "RNAsense": { 4915 "name": "RNAsense", 4916 "version": "1.24.0", 4917 "sha256": "0c3d5694pvwvnandwqy8ikk7477w3myrc4nr13l66m6k6xppfc86", 4918 "depends": ["NBPSeq", "SummarizedExperiment", "ggplot2", "qvalue"] 4919 }, 4920 "RNAseqCovarImpute": { 4921 "name": "RNAseqCovarImpute", 4922 "version": "1.8.0", 4923 "sha256": "0nw3aqjm1yp6vrbx09mmi5wg94wiaha753lp4rkkgifpyzcknd1a", 4924 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "dplyr", "edgeR", "foreach", "limma", "magrittr", "mice", "rlang"] 4925 }, 4926 "ROC": { 4927 "name": "ROC", 4928 "version": "1.86.0", 4929 "sha256": "1n3h77zh7k9mk99g76lb85j5zrk8b0zf8cwgag5xira0d3kggdwm", 4930 "depends": ["knitr"] 4931 }, 4932 "ROCpAI": { 4933 "name": "ROCpAI", 4934 "version": "1.22.0", 4935 "sha256": "0zx18q157xrham37ippaihvzz8ajdcidwrs5pimwy7ds4grz3jcp", 4936 "depends": ["SummarizedExperiment", "boot", "fission", "knitr"] 4937 }, 4938 "ROSeq": { 4939 "name": "ROSeq", 4940 "version": "1.22.0", 4941 "sha256": "01a7wc16j41gl781yan0nqxvrnr9xiqhlbpj5qnp50bhbw0nqxan", 4942 "depends": ["edgeR", "limma", "pbmcapply"] 4943 }, 4944 "ROTS": { 4945 "name": "ROTS", 4946 "version": "2.2.0", 4947 "sha256": "0nw0g72hl519k6d7zwxrpzwbw792w6m0wva0c2cnmk7wz3f4sss9", 4948 "depends": ["Biobase", "BiocParallel", "Rcpp", "lme4"] 4949 }, 4950 "ROntoTools": { 4951 "name": "ROntoTools", 4952 "version": "2.38.0", 4953 "sha256": "02j46cwd3cg7dqgxv93bxh1mqd92sb63vhh8rlwjs46jv1a03ps7", 4954 "depends": ["KEGGREST", "KEGGgraph", "Rgraphviz", "boot", "graph"] 4955 }, 4956 "RPA": { 4957 "name": "RPA", 4958 "version": "1.66.0", 4959 "sha256": "0wmyircvklh9a055aqj4wav1bjzg2r5c7k0kj4smhjln3nl42rd2", 4960 "depends": ["BiocGenerics", "BiocStyle", "affy", "phyloseq", "rmarkdown"] 4961 }, 4962 "RProtoBufLib": { 4963 "name": "RProtoBufLib", 4964 "version": "2.22.0", 4965 "sha256": "096mh27jbmbarjprm82dyxr9x32qsd4vsb3f5x7m06f6g6a6l5kc", 4966 "depends": [] 4967 }, 4968 "RRHO": { 4969 "name": "RRHO", 4970 "version": "1.50.0", 4971 "sha256": "1pdya9fk9c9w8qmq7gj7cbx8a32bm4r1r5i65fp6s3hwpk9k9zca", 4972 "depends": ["VennDiagram"] 4973 }, 4974 "RSVSim": { 4975 "name": "RSVSim", 4976 "version": "1.50.0", 4977 "sha256": "1kcykpbpviiwnin4iap512v1qzlxfx2isxwz1nxjcc8sx75q47ha", 4978 "depends": ["Biostrings", "GenomicRanges", "IRanges", "ShortRead"] 4979 }, 4980 "RSeqAn": { 4981 "name": "RSeqAn", 4982 "version": "1.30.0", 4983 "sha256": "0izhszw6vvhi8g3izcs7868r4ikmw11i5zphqp0prnshdv9scc73", 4984 "depends": ["Rcpp"] 4985 }, 4986 "RTCA": { 4987 "name": "RTCA", 4988 "version": "1.62.0", 4989 "sha256": "0k0sv047laxvmcqh3fd9qhawy8nvl69s0qljs5zfv4zwzz7ksf17", 4990 "depends": ["Biobase", "RColorBrewer", "gtools"] 4991 }, 4992 "RTCGA": { 4993 "name": "RTCGA", 4994 "version": "1.40.0", 4995 "sha256": "18j0kqa1wavhsn6wxx622s021af87kwfnh0yry75b8632fjym8vn", 4996 "depends": ["RCurl", "XML", "assertthat", "data_table", "dplyr", "ggplot2", "ggthemes", "htmltools", "knitr", "purrr", "rmarkdown", "rvest", "scales", "stringi", "survival", "survminer", "viridis", "xml2"] 4997 }, 4998 "RTCGAToolbox": { 4999 "name": "RTCGAToolbox", 5000 "version": "2.40.0", 5001 "sha256": "15h7xahsmpmznnh9n466pbkp094kxaw8x144q4mmy5bx5s7ng6nk", 5002 "depends": ["BiocGenerics", "DelayedArray", "GenomicRanges", "RCurl", "RJSONIO", "RaggedExperiment", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TCGAutils", "data_table", "httr", "rvest", "stringr"] 5003 }, 5004 "RTN": { 5005 "name": "RTN", 5006 "version": "2.34.0", 5007 "sha256": "0pqax97c4v2zbs02m8zpikqgdpjxc44vfhangb9ncvnbpfrpd6vy", 5008 "depends": ["IRanges", "RedeR", "S4Vectors", "SummarizedExperiment", "car", "data_table", "igraph", "limma", "minet", "mixtools", "pheatmap", "pwr", "snow", "viper"] 5009 }, 5010 "RTNduals": { 5011 "name": "RTNduals", 5012 "version": "1.34.0", 5013 "sha256": "04q5gbd2fg6zdkbymqnsb6gapq5b42p3rc4hjrc8xjypflwdgm78", 5014 "depends": ["RTN"] 5015 }, 5016 "RTNsurvival": { 5017 "name": "RTNsurvival", 5018 "version": "1.34.0", 5019 "sha256": "0rh2x9hx9lzqkisxxvqhlk6vk5bni86d3fw1mjv0fsjkdsziky8l", 5020 "depends": ["RColorBrewer", "RTN", "RTNduals", "data_table", "dunn_test", "egg", "ggplot2", "pheatmap", "scales", "survival"] 5021 }, 5022 "RTopper": { 5023 "name": "RTopper", 5024 "version": "1.56.0", 5025 "sha256": "0jl0xp3c60pl5lvn11fscazm7pns2gayix7pf69b29a4n59kxswv", 5026 "depends": ["Biobase", "limma", "multtest"] 5027 }, 5028 "RUCova": { 5029 "name": "RUCova", 5030 "version": "1.2.0", 5031 "sha256": "0nx26i14041gqacx91agrml25vr3phacvzvd0diqyrl39idysqm5", 5032 "depends": ["ComplexHeatmap", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "dplyr", "fastDummies", "ggplot2", "magrittr", "stringr", "tibble", "tidyr", "tidyverse"] 5033 }, 5034 "RUVSeq": { 5035 "name": "RUVSeq", 5036 "version": "1.44.0", 5037 "sha256": "19g3n211dsc019ahpfpwkk4i8clf8jb4fp6wgf7ja3y1xaqmmd5m", 5038 "depends": ["Biobase", "EDASeq", "MASS", "edgeR"] 5039 }, 5040 "RUVcorr": { 5041 "name": "RUVcorr", 5042 "version": "1.42.0", 5043 "sha256": "1wkbpdh8lhkyrxjk9afdyy4l6r393pi7fvaww9zh9mlk78hsr8vx", 5044 "depends": ["BiocParallel", "MASS", "bladderbatch", "corrplot", "gridExtra", "lattice", "psych", "reshape2", "snowfall"] 5045 }, 5046 "RUVnormalize": { 5047 "name": "RUVnormalize", 5048 "version": "1.44.0", 5049 "sha256": "1wa8j3qmc9hz2yrm3gh7qjlfayizc7sw5ay98nincwz96ayiqsdi", 5050 "depends": ["Biobase", "RUVnormalizeData"] 5051 }, 5052 "RVS": { 5053 "name": "RVS", 5054 "version": "1.32.0", 5055 "sha256": "129wq03zy5vcdiv7990i2hvh4pl0mk9zjq7gbay5k5ciynks7jy7", 5056 "depends": ["GENLIB", "R_utils", "gRain", "kinship2", "snpStats"] 5057 }, 5058 "RadioGx": { 5059 "name": "RadioGx", 5060 "version": "2.14.0", 5061 "sha256": "1q76k68zry1cap7is6sxhazrxsv5d49mr863mrzhvnwiz03yzyab", 5062 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "CoreGx", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "assertthat", "caTools", "data_table", "downloader", "magicaxis", "matrixStats", "reshape2", "scales"] 5063 }, 5064 "RaggedExperiment": { 5065 "name": "RaggedExperiment", 5066 "version": "1.34.0", 5067 "sha256": "18mbdd0cd975q2540cdnrfdirc8khg4mqbi8z4zkabal83gzqs2s", 5068 "depends": ["BiocBaseUtils", "BiocGenerics", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "S4Vectors", "Seqinfo", "SummarizedExperiment"] 5069 }, 5070 "RankProd": { 5071 "name": "RankProd", 5072 "version": "3.36.0", 5073 "sha256": "0pvmairya5abkcspwmdh9x0xd46q7sl8pcgzwcqh6gllf6halqqv", 5074 "depends": ["Rmpfr", "gmp"] 5075 }, 5076 "RareVariantVis": { 5077 "name": "RareVariantVis", 5078 "version": "2.38.0", 5079 "sha256": "07afvjijbjfqvbzmg78fpp7ingwvvx9h203c6bczbnvi4n96y1p6", 5080 "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "GenomicScores", "IRanges", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "VariantAnnotation", "googleVis", "gtools", "phastCons100way_UCSC_hg19"] 5081 }, 5082 "Rarr": { 5083 "name": "Rarr", 5084 "version": "1.10.0", 5085 "sha256": "048yv469xrmklmjpz4illrafaf6l56p68jkhsvcjzsx3368bw0w2", 5086 "depends": ["BiocGenerics", "DelayedArray", "R_utils", "curl", "jsonlite", "paws_storage"] 5087 }, 5088 "RbcBook1": { 5089 "name": "RbcBook1", 5090 "version": "1.78.0", 5091 "sha256": "1i39kvws4dr9qryzqf9rl463bpjwvpszk8x6qvi7cpgmrd9zb8pn", 5092 "depends": ["Biobase", "graph", "rpart"] 5093 }, 5094 "Rbec": { 5095 "name": "Rbec", 5096 "version": "1.18.0", 5097 "sha256": "1wgc70g5lkjfx70g9jv1mnxkkm70an8y2zkv3cgn4i1iwmipcvii", 5098 "depends": ["Rcpp", "dada2", "doParallel", "foreach", "ggplot2", "readr"] 5099 }, 5100 "Rbowtie": { 5101 "name": "Rbowtie", 5102 "version": "1.50.0", 5103 "sha256": "13hlr09hshsgwf5694mhrmfxk3nqnl2c58bc4kjsrwngakbi1ziy", 5104 "depends": [] 5105 }, 5106 "Rbowtie2": { 5107 "name": "Rbowtie2", 5108 "version": "2.16.0", 5109 "sha256": "0gjicqyl3kmadm0ki2n22231dcx5dijj5wz50fkyc6n0a3xvgsx5", 5110 "depends": ["Rsamtools", "magrittr"] 5111 }, 5112 "RbowtieCuda": { 5113 "name": "RbowtieCuda", 5114 "version": "1.2.0", 5115 "sha256": "05ca0wn7z44rkj885l5h1ybsjn4kl2x1gy9cy98p63gws1xwq6h0", 5116 "depends": [] 5117 }, 5118 "Rbwa": { 5119 "name": "Rbwa", 5120 "version": "1.14.0", 5121 "sha256": "1rkx6smq6cpi3ghcygvwvgq49d0grn3m0sw5jnl0mxqm8ygfr290", 5122 "depends": [] 5123 }, 5124 "RcisTarget": { 5125 "name": "RcisTarget", 5126 "version": "1.29.0", 5127 "sha256": "0y028c8vrfcqy9ddn7p4y285bjb3hw5n1rwax4ggwbf18cfk1ql2", 5128 "depends": ["AUCell", "BiocGenerics", "GSEABase", "GenomeInfoDb", "GenomicRanges", "R_utils", "S4Vectors", "SummarizedExperiment", "arrow", "data_table", "dplyr", "tibble", "zoo"] 5129 }, 5130 "Rcollectl": { 5131 "name": "Rcollectl", 5132 "version": "1.10.0", 5133 "sha256": "0inkixnlvfs5qp8ywffaamvhk3mz2mcl3kcvvzs49jf4j7376lbh", 5134 "depends": ["ggplot2", "lubridate", "processx"] 5135 }, 5136 "Rcpi": { 5137 "name": "Rcpi", 5138 "version": "1.46.0", 5139 "sha256": "1dx8im6525sj8496czmx346cw30ijyj9i8p0jzsvssw6994pnyz4", 5140 "depends": ["Biostrings", "GOSemSim", "curl", "doParallel", "foreach", "httr2", "jsonlite", "rlang"] 5141 }, 5142 "Rcwl": { 5143 "name": "Rcwl", 5144 "version": "1.26.0", 5145 "sha256": "0a6i3g3da7zkrxqphvaamg10f3s7qjynhn65w3v342gdbbk67b1w", 5146 "depends": ["BiocParallel", "DiagrammeR", "R_utils", "S4Vectors", "basilisk", "batchtools", "codetools", "shiny", "yaml"] 5147 }, 5148 "RcwlPipelines": { 5149 "name": "RcwlPipelines", 5150 "version": "1.26.0", 5151 "sha256": "01c95nxvwi6lhbvc33a3797hsvq7w6rswnxwg5v44fc1zg002mlf", 5152 "depends": ["BiocFileCache", "Rcwl", "S4Vectors", "git2r", "httr", "rappdirs"] 5153 }, 5154 "Rdisop": { 5155 "name": "Rdisop", 5156 "version": "1.70.0", 5157 "sha256": "0jkm610772hyg63q5wmvrbwcbbyfzryii6ab37fv79qy7k56l8wn", 5158 "depends": ["Rcpp"] 5159 }, 5160 "ReUseData": { 5161 "name": "ReUseData", 5162 "version": "1.10.0", 5163 "sha256": "1xzi5vnr7k6ijssp66ii95nswyly1c8yc76gqw6vhrgyzawwh503", 5164 "depends": ["BiocFileCache", "Rcwl", "RcwlPipelines", "S4Vectors", "basilisk", "jsonlite", "yaml"] 5165 }, 5166 "ReactomeGSA": { 5167 "name": "ReactomeGSA", 5168 "version": "1.24.0", 5169 "sha256": "1nqz3xmxriybdx6yvdhah2sxz8mn44gplgssdcw5f9nl7aww9a0k", 5170 "depends": ["Biobase", "BiocSingular", "RColorBrewer", "SummarizedExperiment", "dplyr", "ggplot2", "gplots", "httr", "igraph", "jsonlite", "progress", "tidyr"] 5171 }, 5172 "ReactomePA": { 5173 "name": "ReactomePA", 5174 "version": "1.54.0", 5175 "sha256": "0vh8knsczh537r9qk6h3jyabd6x4c4g2j7fz8qsflhl7bs20n4h9", 5176 "depends": ["AnnotationDbi", "DOSE", "enrichplot", "ggplot2", "ggraph", "graphite", "gson", "igraph", "reactome_db", "yulab_utils"] 5177 }, 5178 "ReadqPCR": { 5179 "name": "ReadqPCR", 5180 "version": "1.56.0", 5181 "sha256": "1m5yh01f3xgvs5fbyxaagfx3q25sxc77z9mgr293rq4436zvsgyy", 5182 "depends": ["Biobase"] 5183 }, 5184 "RedeR": { 5185 "name": "RedeR", 5186 "version": "3.6.0", 5187 "sha256": "0sqqhr9blgarvi7dxyxmk0ikj9grqj9zbz9yqb55qhr67mzl3d3i", 5188 "depends": ["igraph", "scales"] 5189 }, 5190 "RedisParam": { 5191 "name": "RedisParam", 5192 "version": "1.12.0", 5193 "sha256": "0d88g6mxlifc86ar2695p5gjrbafc0vgjmbxayv9x0h5b0c9hg8z", 5194 "depends": ["BiocParallel", "futile_logger", "redux", "withr"] 5195 }, 5196 "ReducedExperiment": { 5197 "name": "ReducedExperiment", 5198 "version": "1.2.0", 5199 "sha256": "114hwvqpfw0lf4hxjdmqsvmlsllzxvf8s3843nklz0pnhw8a1hxr", 5200 "depends": ["BiocGenerics", "BiocParallel", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "WGCNA", "biomaRt", "car", "clusterProfiler", "ggplot2", "ica", "lme4", "lmerTest", "moments", "msigdbr", "patchwork", "pheatmap"] 5201 }, 5202 "RegEnrich": { 5203 "name": "RegEnrich", 5204 "version": "1.20.0", 5205 "sha256": "1q40yk4lmnyqwzj2mjrhl6gb03r20kyw8dy8543n5isbgd24i08d", 5206 "depends": ["BiocParallel", "BiocSet", "BiocStyle", "DESeq2", "DOSE", "S4Vectors", "SummarizedExperiment", "WGCNA", "dplyr", "fgsea", "ggplot2", "limma", "magrittr", "randomForest", "reshape2", "tibble"] 5207 }, 5208 "RegionalST": { 5209 "name": "RegionalST", 5210 "version": "1.8.0", 5211 "sha256": "19cghwn3jff5d8zsswfq1rnj3fxc6w86n4xmxdyzw2ja7868lmv0", 5212 "depends": ["BayesSpace", "BiocStyle", "RColorBrewer", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "TOAST", "assertthat", "colorspace", "dplyr", "fgsea", "ggplot2", "gridExtra", "magrittr", "scater", "shiny", "tibble"] 5213 }, 5214 "ReportingTools": { 5215 "name": "ReportingTools", 5216 "version": "2.50.0", 5217 "sha256": "09bj554ygii77c04yf10lvsnkg2r3lngi238rh5zgwadi47rcy9w", 5218 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "Category", "DESeq2", "GOstats", "GSEABase", "IRanges", "PFAM_db", "R_utils", "XML", "annotate", "edgeR", "ggbio", "ggplot2", "hwriter", "knitr", "lattice", "limma"] 5219 }, 5220 "ResidualMatrix": { 5221 "name": "ResidualMatrix", 5222 "version": "1.20.0", 5223 "sha256": "14qx2yb0ahfjjmqlcirar51l5if8wh6v7g95bvr3n2ak2i3arzhb", 5224 "depends": ["DelayedArray", "Matrix", "S4Vectors"] 5225 }, 5226 "RgnTX": { 5227 "name": "RgnTX", 5228 "version": "1.11.1", 5229 "sha256": "1va4nw2gbhkhrryfglc0chgp9ncgmjk8852sf6vgf4fq8jqla5a2", 5230 "depends": ["GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "TxDb_Hsapiens_UCSC_hg19_knownGene", "ggplot2", "regioneR"] 5231 }, 5232 "Rgraphviz": { 5233 "name": "Rgraphviz", 5234 "version": "2.54.0", 5235 "sha256": "0mjv95nwfsak6wk0dnjp75n9xklynrbsvhhk6i3xaifgyg0d18pr", 5236 "depends": ["graph"] 5237 }, 5238 "Rhdf5lib": { 5239 "name": "Rhdf5lib", 5240 "version": "1.32.0", 5241 "sha256": "1i0g82j7q6j1hp9c8vc6sv50ph1n028hpc8wfsifx4cc1w5hhvmy", 5242 "depends": [] 5243 }, 5244 "Rhisat2": { 5245 "name": "Rhisat2", 5246 "version": "1.26.0", 5247 "sha256": "01i6085rl7in0xslm872m1ahnj39hks3b2frplyxw6i5lznk66bf", 5248 "depends": ["GenomicRanges", "SGSeq", "txdbmaker"] 5249 }, 5250 "Rhtslib": { 5251 "name": "Rhtslib", 5252 "version": "3.6.0", 5253 "sha256": "14k6v897ccah78lw41wd4c37wz048l2963sv3cvvgvrrpbgw0pwb", 5254 "depends": [] 5255 }, 5256 "RiboCrypt": { 5257 "name": "RiboCrypt", 5258 "version": "1.16.0", 5259 "sha256": "1l6lmr7w8sq6g95hqi9n4cdg9v8gbs2bscd4s57dlrnbx46y4ncy", 5260 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "ComplexHeatmap", "DT", "GenomicFeatures", "GenomicRanges", "IRanges", "NGLVieweR", "ORFik", "RCurl", "Seqinfo", "bslib", "cowplot", "crosstalk", "data_table", "dplyr", "fst", "ggplot2", "htmlwidgets", "httr", "jsonlite", "knitr", "markdown", "plotly", "rclipboard", "rlang", "rtracklayer", "shiny", "shinyWidgets", "shinycssloaders", "shinyhelper", "shinyjqui", "shinyjs", "stringr", "writexl"] 5261 }, 5262 "RiboDiPA": { 5263 "name": "RiboDiPA", 5264 "version": "1.18.0", 5265 "sha256": "1cbfwwm1i67qhk8rnqvgpf18gz4dcmagxs06nff76r96kfvyp0gg", 5266 "depends": ["BiocFileCache", "BiocGenerics", "DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rcpp", "Rsamtools", "S4Vectors", "data_table", "doParallel", "elitism", "foreach", "ggplot2", "matrixStats", "qvalue", "reldist", "txdbmaker"] 5267 }, 5268 "RiboProfiling": { 5269 "name": "RiboProfiling", 5270 "version": "1.39.1", 5271 "sha256": "0yqmk7cgfahyiy4gcrfr4iyf9sa6sl42h41xaj65b4dx6mhgqrs9", 5272 "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "data_table", "ggbio", "ggplot2", "plyr", "reshape2", "rtracklayer", "sqldf"] 5273 }, 5274 "Rigraphlib": { 5275 "name": "Rigraphlib", 5276 "version": "1.2.0", 5277 "sha256": "190h2gjwy913422c0j3b368bvf801nggqx6a620z05ivw2w1yad4", 5278 "depends": ["biocmake"] 5279 }, 5280 "Rmagpie": { 5281 "name": "Rmagpie", 5282 "version": "1.66.0", 5283 "sha256": "12rkh9xwxgnpa46skin89z2w0xi352k539n7w4ybqbdlwfwwvqk3", 5284 "depends": ["Biobase", "e1071", "kernlab", "pamr"] 5285 }, 5286 "Rmmquant": { 5287 "name": "Rmmquant", 5288 "version": "1.28.0", 5289 "sha256": "1qwch1kgws7zvgvxavyh885i0jfs24yl9qnmaav1xycl5zmw8dml", 5290 "depends": ["BiocStyle", "DESeq2", "GenomicRanges", "Rcpp", "S4Vectors", "SummarizedExperiment", "TBX20BamSubset", "TxDb_Mmusculus_UCSC_mm9_knownGene", "apeglm", "devtools", "org_Mm_eg_db"] 5291 }, 5292 "RnBeads": { 5293 "name": "RnBeads", 5294 "version": "2.28.0", 5295 "sha256": "00vfljydr8f9y1d4vh08v2ziwyr7gb36kqzc5xc0nb3f2w66f80d", 5296 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "cluster", "ff", "fields", "ggplot2", "gplots", "gridExtra", "illuminaio", "limma", "matrixStats", "methylumi", "plyr", "reshape2"] 5297 }, 5298 "RnaSeqSampleSize": { 5299 "name": "RnaSeqSampleSize", 5300 "version": "2.20.0", 5301 "sha256": "18s1xqf3sfj0cicypq18d39znx5prsr5j3incgxrhh7nlcq2llkq", 5302 "depends": ["KEGGREST", "Rcpp", "RnaSeqSampleSizeData", "SummarizedExperiment", "biomaRt", "dplyr", "edgeR", "ggplot2", "ggpubr", "heatmap3", "matlab", "recount", "tidyr", "tidyselect"] 5303 }, 5304 "Rnits": { 5305 "name": "Rnits", 5306 "version": "1.44.0", 5307 "sha256": "0a6sqz5bc605sw8wvz0jsy7xly8cz992vc9a667xkxsf6xa4a3wl", 5308 "depends": ["Biobase", "affy", "boot", "ggplot2", "impute", "limma", "qvalue", "reshape2"] 5309 }, 5310 "RolDE": { 5311 "name": "RolDE", 5312 "version": "1.14.0", 5313 "sha256": "1bn0h9v27azw9gmdnbsa66mqg9jbw85cbcb0zv8kmxmycvgxnxwa", 5314 "depends": ["ROTS", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "matrixStats", "nlme", "qvalue", "rngtools"] 5315 }, 5316 "Rqc": { 5317 "name": "Rqc", 5318 "version": "1.44.0", 5319 "sha256": "1kprj05y5y5k78gdsffn0j9zjg8c466c9x50fqy7mfps4z9rdcwi", 5320 "depends": ["BiocGenerics", "BiocParallel", "BiocStyle", "Biostrings", "GenomicAlignments", "GenomicFiles", "IRanges", "Rcpp", "Rsamtools", "S4Vectors", "ShortRead", "biovizBase", "ggplot2", "knitr", "markdown", "plyr", "reshape2", "shiny"] 5321 }, 5322 "Rsamtools": { 5323 "name": "Rsamtools", 5324 "version": "2.26.0", 5325 "sha256": "1sbb95xknaj2jks0wlcj1zr43i23l27j5mjsihyk9q1kxybhmnlw", 5326 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomicRanges", "IRanges", "Rhtslib", "S4Vectors", "Seqinfo", "XVector", "bitops"] 5327 }, 5328 "Rsubread": { 5329 "name": "Rsubread", 5330 "version": "2.24.0", 5331 "sha256": "14i2qm3wgzl8kj3d2kkppzlvvpkn27qggz6b44kwxhi5ns8rn7zq", 5332 "depends": ["Matrix"] 5333 }, 5334 "Rtpca": { 5335 "name": "Rtpca", 5336 "version": "1.20.0", 5337 "sha256": "0971zm4rcva3q6bdz5zgbm5y9hsjhz5x52sjvaa7i624x4ajs1z3", 5338 "depends": ["Biobase", "dplyr", "fdrtool", "ggplot2", "pROC", "tibble", "tidyr"] 5339 }, 5340 "Rvisdiff": { 5341 "name": "Rvisdiff", 5342 "version": "1.8.0", 5343 "sha256": "0ayzc1zprrlkv1hvzrc8x9h25v5rmfz1kkrkszvbn6gka7ka2zqf", 5344 "depends": ["edgeR"] 5345 }, 5346 "S4Arrays": { 5347 "name": "S4Arrays", 5348 "version": "1.10.0", 5349 "sha256": "1vbvr0vfwl36i7dv09ibzs7mkfyzlzfl475rrkss377zsz7gbsjh", 5350 "depends": ["BiocGenerics", "IRanges", "Matrix", "S4Vectors", "abind"] 5351 }, 5352 "S4Vectors": { 5353 "name": "S4Vectors", 5354 "version": "0.48.0", 5355 "sha256": "1vs1n92d915gpvrl4y867gym9q1rsz5b0pkajndy58c329zx4m2v", 5356 "depends": ["BiocGenerics"] 5357 }, 5358 "SAIGEgds": { 5359 "name": "SAIGEgds", 5360 "version": "2.10.0", 5361 "sha256": "0y4zkdf6khicaxbm7d98pvbd083c4624cc290xc1sssxf8nxrahn", 5362 "depends": ["CompQuadForm", "Matrix", "Rcpp", "RcppArmadillo", "RcppParallel", "SKAT", "SeqArray", "gdsfmt", "survey"] 5363 }, 5364 "SANTA": { 5365 "name": "SANTA", 5366 "version": "2.46.0", 5367 "sha256": "0saxpxbxwyzl4a8w7z550df5x1gzpg56si7hzv6r6v9arcc39i50", 5368 "depends": ["Matrix", "igraph"] 5369 }, 5370 "SBGNview": { 5371 "name": "SBGNview", 5372 "version": "1.24.0", 5373 "sha256": "1qyxd55c1w8kv5dchjcl6kfg96sq52y7fvinxssq9dacwk0p698w", 5374 "depends": ["AnnotationDbi", "KEGGREST", "Rdpack", "SBGNview_data", "SummarizedExperiment", "bookdown", "httr", "igraph", "knitr", "pathview", "rmarkdown", "rsvg", "xml2"] 5375 }, 5376 "SBMLR": { 5377 "name": "SBMLR", 5378 "version": "2.6.0", 5379 "sha256": "0qy698n59i9c4lhlc1nhs7p9pcg1c7y818vyw23piyk8x27rd2wq", 5380 "depends": ["XML", "deSolve"] 5381 }, 5382 "SC3": { 5383 "name": "SC3", 5384 "version": "1.38.0", 5385 "sha256": "1ysxbarqrw8pbg2fm66nsyjxshi0c14svydwc3yj2ldlv25n7kmi", 5386 "depends": ["BiocGenerics", "ROCR", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "WriteXLS", "cluster", "doParallel", "doRNG", "e1071", "foreach", "ggplot2", "pheatmap", "robustbase", "rrcov", "shiny"] 5387 }, 5388 "SCAN_UPC": { 5389 "name": "SCAN.UPC", 5390 "version": "2.52.0", 5391 "sha256": "0kvzg4i7yl0d1p0plwzbisl6z3kjn46avaa86g5y9jxj4vwhgb9p", 5392 "depends": ["Biobase", "Biostrings", "GEOquery", "IRanges", "MASS", "affy", "affyio", "foreach", "oligo", "sva"] 5393 }, 5394 "SCANVIS": { 5395 "name": "SCANVIS", 5396 "version": "1.24.0", 5397 "sha256": "10a7iw5iqmnlhn74000gbaqnbkp98l0ar4cin8fqgrbmj5fmm0ha", 5398 "depends": ["IRanges", "RCurl", "plotrix", "rtracklayer"] 5399 }, 5400 "SCArray": { 5401 "name": "SCArray", 5402 "version": "1.18.0", 5403 "sha256": "1bxbjl5445glqj6vsl6i0z1rrkc6k91glhg343ykzz2hhjz6xifd", 5404 "depends": ["BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "Matrix", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "gdsfmt"] 5405 }, 5406 "SCArray_sat": { 5407 "name": "SCArray.sat", 5408 "version": "1.9.0", 5409 "sha256": "0yd5pinqbdi5pq1vcbabwqnwhw3vrk3qbdyrqi82hib5zqxzw9zr", 5410 "depends": ["BiocGenerics", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "S4Vectors", "SCArray", "Seurat", "SeuratObject", "SummarizedExperiment", "gdsfmt"] 5411 }, 5412 "SCBN": { 5413 "name": "SCBN", 5414 "version": "1.28.0", 5415 "sha256": "0snnmajjqlrnpcib472i0g9kbsxw9f63gxjj0i58x4xpw9skia57", 5416 "depends": [] 5417 }, 5418 "SCFA": { 5419 "name": "SCFA", 5420 "version": "1.20.0", 5421 "sha256": "0p9i44qbff4xwrr7l1v9p7limwn7ahdx0ca47alqqz6nkig36kbr", 5422 "depends": ["BiocParallel", "Matrix", "RhpcBLASctl", "cluster", "coro", "glmnet", "igraph", "matrixStats", "psych", "survival", "torch"] 5423 }, 5424 "SCOPE": { 5425 "name": "SCOPE", 5426 "version": "1.22.0", 5427 "sha256": "0jf4xd23cx4xafjzcd7jdlk2m57sa3v62fc3zlh71gpz9vbgc82n", 5428 "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "Biostrings", "DNAcopy", "DescTools", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "doParallel", "foreach", "gplots"] 5429 }, 5430 "SCnorm": { 5431 "name": "SCnorm", 5432 "version": "1.32.0", 5433 "sha256": "17shqmq81na16wkd7dfjajrhv0mi8zmb9nf5cjns3s4ja2392pja", 5434 "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cluster", "data_table", "forcats", "ggplot2", "moments", "quantreg"] 5435 }, 5436 "SDAMS": { 5437 "name": "SDAMS", 5438 "version": "1.30.0", 5439 "sha256": "1arr0ld2nr6iqqc1h9v35cpn5zllbbqbbhjza6m2jrwgx7b6j973", 5440 "depends": ["SummarizedExperiment", "qvalue", "trust"] 5441 }, 5442 "SELEX": { 5443 "name": "SELEX", 5444 "version": "1.42.0", 5445 "sha256": "0mpggx9dbq16s5c7qpx5rgbjim5a9hs899fmf65v1slgbnikwazq", 5446 "depends": ["Biostrings", "rJava"] 5447 }, 5448 "SETA": { 5449 "name": "SETA", 5450 "version": "1.0.0", 5451 "sha256": "00i8cg086iv31bri3b3pwiz8ajxyxnnszarinsdcr3kan2gaaxa6", 5452 "depends": ["MASS", "Matrix", "SingleCellExperiment", "dplyr", "rlang", "tidygraph"] 5453 }, 5454 "SEraster": { 5455 "name": "SEraster", 5456 "version": "1.2.0", 5457 "sha256": "0ff953kwyq9flmnbpyyfal4n8p4j29ha1c4blr1l317m7sj6idcf", 5458 "depends": ["BiocParallel", "Matrix", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "rearrr", "sf"] 5459 }, 5460 "SEtools": { 5461 "name": "SEtools", 5462 "version": "1.24.0", 5463 "sha256": "1j161pgm0gb59hw8x8r60zxh1xn20wp8qkw3ls6pvryjgxiqm1ky", 5464 "depends": ["BiocParallel", "DESeq2", "Matrix", "S4Vectors", "SummarizedExperiment", "circlize", "data_table", "edgeR", "openxlsx", "pheatmap", "sechm", "sva"] 5465 }, 5466 "SGSeq": { 5467 "name": "SGSeq", 5468 "version": "1.44.0", 5469 "sha256": "04sk9q7v22p1hc7znaa2fn390y5pn1nj0ayjb0b3746klsyxxc11", 5470 "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RUnit", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "igraph", "rtracklayer"] 5471 }, 5472 "SIAMCAT": { 5473 "name": "SIAMCAT", 5474 "version": "2.14.0", 5475 "sha256": "0czzgi1kxy4la4kbw7s6px53lp6wzkdmqlpc675q90c1nmqja1y1", 5476 "depends": ["LiblineaR", "PRROC", "RColorBrewer", "beanplot", "corrplot", "glmnet", "gridBase", "gridExtra", "infotheo", "lgr", "lmerTest", "matrixStats", "mlr3", "mlr3learners", "mlr3tuning", "pROC", "paradox", "phyloseq", "progress", "scales", "stringr"] 5477 }, 5478 "SICtools": { 5479 "name": "SICtools", 5480 "version": "1.40.0", 5481 "sha256": "0qrs93igg20i2zk7gcmgw54q0khp9ak7b0q6bvm7l3hjkl0lipdb", 5482 "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "doParallel", "matrixStats", "plyr", "stringr"] 5483 }, 5484 "SIM": { 5485 "name": "SIM", 5486 "version": "1.80.0", 5487 "sha256": "1hy4ik6mac7rqchcr3pssj41lsgkfcw0mifkgkhw3sw43bfnh611", 5488 "depends": ["globaltest", "quantreg", "quantsmooth"] 5489 }, 5490 "SIMAT": { 5491 "name": "SIMAT", 5492 "version": "1.42.0", 5493 "sha256": "1bwwip4wszs39yhdpwl14vcfrlq1aav1gmiijwnx5fl77vcfais5", 5494 "depends": ["Rcpp", "ggplot2", "mzR", "reshape2"] 5495 }, 5496 "SIMD": { 5497 "name": "SIMD", 5498 "version": "1.28.0", 5499 "sha256": "100z1ib7s739piwazppjrg7jpxfmqwd2kwahwxkjxj14pbc5gfhq", 5500 "depends": ["edgeR", "methylMnM", "statmod"] 5501 }, 5502 "SIMLR": { 5503 "name": "SIMLR", 5504 "version": "1.36.0", 5505 "sha256": "1fxd14kf4ai2hm9nxragqisckca5spkk8slc4biy2viqj90nvvy2", 5506 "depends": ["Matrix", "RSpectra", "Rcpp", "RcppAnnoy", "pracma"] 5507 }, 5508 "SLqPCR": { 5509 "name": "SLqPCR", 5510 "version": "1.76.0", 5511 "sha256": "0861cnnq1yybmq7gac2n2q6gfap3sfadacpdxzc73iqx54a6p2gf", 5512 "depends": [] 5513 }, 5514 "SMAD": { 5515 "name": "SMAD", 5516 "version": "1.26.0", 5517 "sha256": "0hh4lxrylmrn50211n3ggc2n4qgbcwh1qxrqbj7xwr2ficxym28b", 5518 "depends": ["Rcpp", "RcppAlgos", "dplyr", "magrittr", "tidyr"] 5519 }, 5520 "SMITE": { 5521 "name": "SMITE", 5522 "version": "1.38.0", 5523 "sha256": "01x1wla1pqb361c75fjm4c5k7aajlw3l82ln5bbv9b8zmyjj54sv", 5524 "depends": ["AnnotationDbi", "BioNet", "Biobase", "GenomicRanges", "Hmisc", "IRanges", "KEGGREST", "S4Vectors", "geneLenDataBase", "ggplot2", "goseq", "igraph", "org_Hs_eg_db", "plyr", "reactome_db", "scales"] 5525 }, 5526 "SNAGEE": { 5527 "name": "SNAGEE", 5528 "version": "1.50.0", 5529 "sha256": "1zpk0nklf83vjr1wganx0qzkz0ypkd485zffgpr726zcz14bixjl", 5530 "depends": ["SNAGEEdata"] 5531 }, 5532 "SNPRelate": { 5533 "name": "SNPRelate", 5534 "version": "1.44.0", 5535 "sha256": "1xzvrasba81a51wc48gdh82qga9a43hjx79cdw7jgb9vsn6w4iha", 5536 "depends": ["RhpcBLASctl", "gdsfmt"] 5537 }, 5538 "SNPediaR": { 5539 "name": "SNPediaR", 5540 "version": "1.36.0", 5541 "sha256": "1kis54hb6nm2hbyrpxf5cr02a1iq2bdgnxx7zak389mrsy54gv1n", 5542 "depends": ["RCurl", "jsonlite"] 5543 }, 5544 "SNPhood": { 5545 "name": "SNPhood", 5546 "version": "1.40.0", 5547 "sha256": "1fy444c7qp1d47321jc4q5mzki53angwrxp2j0b9bswpi7aw79vj", 5548 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "checkmate", "cluster", "data_table", "ggplot2", "gridExtra", "lattice", "reshape2", "scales"] 5549 }, 5550 "SOMNiBUS": { 5551 "name": "SOMNiBUS", 5552 "version": "1.18.0", 5553 "sha256": "1ccskmmrcpl28amnh7nj2pkpa00vahrhg7c61vdgrl7mrym1kd9c", 5554 "depends": ["BiocManager", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "VGAM", "annotatr", "bsseq", "data_table", "ggplot2", "mgcv", "reshape2", "rtracklayer", "tidyr", "yaml"] 5555 }, 5556 "SPEM": { 5557 "name": "SPEM", 5558 "version": "1.50.0", 5559 "sha256": "0js9l4rgqbbd95hn872mfz27hag5yg5jp58rbvydxjz4w9x8883b", 5560 "depends": ["Biobase", "Rsolnp"] 5561 }, 5562 "SPIA": { 5563 "name": "SPIA", 5564 "version": "2.62.0", 5565 "sha256": "0dl139352p1xl72i7189y40hfk2i6q4nf2s01rwdjgris9sihc2a", 5566 "depends": ["KEGGgraph"] 5567 }, 5568 "SPIAT": { 5569 "name": "SPIAT", 5570 "version": "1.12.0", 5571 "sha256": "1y5j6sh5ls10w491sjrb99m80mwh29bdwkg97r3ykyh09wk2w5dq", 5572 "depends": ["RANN", "SpatialExperiment", "SummarizedExperiment", "apcluster", "dbscan", "dittoSeq", "dplyr", "ggplot2", "gridExtra", "gtools", "mmand", "pracma", "raster", "reshape2", "rlang", "sp", "spatstat_explore", "spatstat_geom", "tibble", "vroom"] 5573 }, 5574 "SPICEY": { 5575 "name": "SPICEY", 5576 "version": "1.0.0", 5577 "sha256": "1qvwn27dnvyal8kjk5aj619ln4p64jnpi8b73cp4jjad67cibzlw", 5578 "depends": ["AnnotationDbi", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "S4Vectors", "cowplot", "dplyr", "ggplot2", "scales", "tibble", "tidyr"] 5579 }, 5580 "SPLINTER": { 5581 "name": "SPLINTER", 5582 "version": "1.36.0", 5583 "sha256": "05iikzwbk7qaw37p1kg18shwk6p84rvhxdnjrvi30bla20abgh2w", 5584 "depends": ["BSgenome_Mmusculus_UCSC_mm9", "Biostrings", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "Seqinfo", "biomaRt", "ggplot2", "googleVis", "plyr", "pwalign", "seqLogo", "stringr"] 5585 }, 5586 "SPONGE": { 5587 "name": "SPONGE", 5588 "version": "1.32.0", 5589 "sha256": "1xqynqv006jz4kdz5iq9hmpqdrc32zi2lk50gmyw0ckgixapyxp4", 5590 "depends": ["Biobase", "ComplexHeatmap", "MASS", "MetBrewer", "biomaRt", "caret", "cvms", "data_table", "doRNG", "dplyr", "expm", "foreach", "gRbase", "ggplot2", "ggpubr", "ggridges", "glmnet", "igraph", "iterators", "logging", "ppcor", "randomForest", "rlang", "stringr", "tidyr", "tidyverse", "tnet"] 5591 }, 5592 "SPOTlight": { 5593 "name": "SPOTlight", 5594 "version": "1.14.0", 5595 "sha256": "1bnwss0rk2psy0l0imlgvvb6vq76f0kjzsr9nc5g9x001k7ic5n8", 5596 "depends": ["Matrix", "Rcpp", "RcppEigen", "SingleCellExperiment", "ggplot2", "sparseMatrixStats"] 5597 }, 5598 "SPsimSeq": { 5599 "name": "SPsimSeq", 5600 "version": "1.20.0", 5601 "sha256": "106apmdmd8cclfdfbx8n9mkniwvaz3h7psjryylbsxr1cqbxac1a", 5602 "depends": ["Hmisc", "SingleCellExperiment", "WGCNA", "edgeR", "fitdistrplus", "limma", "mvtnorm", "phyloseq"] 5603 }, 5604 "SRAdb": { 5605 "name": "SRAdb", 5606 "version": "1.72.0", 5607 "sha256": "0wkma09cj3x4wwk7847ka2g0gqpch8dg0hqcs63p58wx2wmprfq4", 5608 "depends": ["RCurl", "RSQLite", "R_utils", "graph"] 5609 }, 5610 "STADyUM": { 5611 "name": "STADyUM", 5612 "version": "1.0.0", 5613 "sha256": "145qwzg0n88jdlgr0pfvnhmrk92f6hkfl3sq31vi0b3rlmazaw1f", 5614 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "Rcpp", "S4Vectors", "data_table", "dplyr", "ggplot2", "plyranges", "progress", "purrr", "rlang", "rtracklayer", "tibble", "tidyr"] 5615 }, 5616 "STATegRa": { 5617 "name": "STATegRa", 5618 "version": "1.46.0", 5619 "sha256": "010ik7iv37dcasbz75j9150l2vkxcwzkhrvf9r0if8wrg1n26m81", 5620 "depends": ["Biobase", "MASS", "affy", "calibrate", "edgeR", "foreach", "ggplot2", "gplots", "gridExtra", "limma"] 5621 }, 5622 "STRINGdb": { 5623 "name": "STRINGdb", 5624 "version": "2.22.0", 5625 "sha256": "1wr0jl0yk1739yyy2j5b9l3kc5rmbxwpky2hmpv4nq0ykz9lbxqx", 5626 "depends": ["RColorBrewer", "gplots", "hash", "httr", "igraph", "plotrix", "plyr", "png", "sqldf"] 5627 }, 5628 "SUITOR": { 5629 "name": "SUITOR", 5630 "version": "1.12.0", 5631 "sha256": "161dvlf9jsa1334dbs71ddy6bk4yiwhx47c5yhb6xkswjl6zm0q3", 5632 "depends": ["BiocParallel", "ggplot2"] 5633 }, 5634 "SVMDO": { 5635 "name": "SVMDO", 5636 "version": "1.10.0", 5637 "sha256": "0yjsn8ipz9fq6cy8z1f9yxd6zdha6zj4b6db2kms5cjrclggy98y", 5638 "depends": ["AnnotationDbi", "BSDA", "DOSE", "DT", "SummarizedExperiment", "caTools", "caret", "data_table", "dplyr", "e1071", "golem", "klaR", "nortest", "org_Hs_eg_db", "shiny", "shinyFiles", "shinytitle", "sjmisc", "survival"] 5639 }, 5640 "SVP": { 5641 "name": "SVP", 5642 "version": "1.2.0", 5643 "sha256": "0735sjwwb00y77f7wai6aw4gqvjvac6s8979ppy3g7av46wmi12l", 5644 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "DelayedMatrixStats", "Matrix", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cli", "deldir", "dplyr", "dqrng", "fastmatch", "ggfun", "ggplot2", "ggstar", "ggtree", "pracma", "rlang", "withr"] 5645 }, 5646 "SWATH2stats": { 5647 "name": "SWATH2stats", 5648 "version": "1.40.0", 5649 "sha256": "1ds8ra2jr31hdp2ym65vgqsp79ipgv01q6qrhx4rnsn2jh95gvlq", 5650 "depends": ["biomaRt", "data_table", "ggplot2", "reshape2"] 5651 }, 5652 "SamSPECTRAL": { 5653 "name": "SamSPECTRAL", 5654 "version": "1.64.0", 5655 "sha256": "1ncxkzydr5d0xca7jikif6s68m5ah6bnk7qg45cf1svicar4k0j1", 5656 "depends": [] 5657 }, 5658 "SanityR": { 5659 "name": "SanityR", 5660 "version": "1.0.0", 5661 "sha256": "0a7zayilxgw7fzqqk8b9f3q6r3chagkmy5bxyai0ylsxg49202sw", 5662 "depends": ["BiocGenerics", "BiocParallel", "MatrixGenerics", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "scuttle"] 5663 }, 5664 "Scale4C": { 5665 "name": "Scale4C", 5666 "version": "1.32.0", 5667 "sha256": "063h796ywzzp92avhvjhdbmzd7z4a3rm2rvb60sigkbbb1636scj", 5668 "depends": ["GenomicRanges", "IRanges", "SummarizedExperiment", "smoothie"] 5669 }, 5670 "ScaledMatrix": { 5671 "name": "ScaledMatrix", 5672 "version": "1.18.0", 5673 "sha256": "1bzbqszkfwwa8jgd5d0yb8jx84g400svfk7b0vrm45n6vng9279g", 5674 "depends": ["DelayedArray", "Matrix", "S4Vectors"] 5675 }, 5676 "Sconify": { 5677 "name": "Sconify", 5678 "version": "1.30.0", 5679 "sha256": "1py4q8w8y8f1sr4qrpaknmw52sc8sls5zhm2ycrsdkhfwyswcvvm", 5680 "depends": ["FNN", "Rtsne", "dplyr", "flowCore", "ggplot2", "magrittr", "readr", "tibble"] 5681 }, 5682 "SemDist": { 5683 "name": "SemDist", 5684 "version": "1.44.0", 5685 "sha256": "0hlfyfkiizfyh1fy0b5xy19k3253ib0m1fqb542rdayzfk8qhn48", 5686 "depends": ["AnnotationDbi", "GO_db", "annotate"] 5687 }, 5688 "SeqArray": { 5689 "name": "SeqArray", 5690 "version": "1.50.0", 5691 "sha256": "0p749sf2smc8j59qs5k3vkxlf5h2zws8q40vrnhv1svl1j1gc17d", 5692 "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "digest", "gdsfmt"] 5693 }, 5694 "SeqGSEA": { 5695 "name": "SeqGSEA", 5696 "version": "1.50.0", 5697 "sha256": "02xzwpn95q1dp7a2hd2rhrs7zd8z64d7f6w7ksabxbm3vsmwzrlm", 5698 "depends": ["Biobase", "DESeq2", "biomaRt", "doParallel"] 5699 }, 5700 "SeqGate": { 5701 "name": "SeqGate", 5702 "version": "1.20.0", 5703 "sha256": "1yzq4clc9xvh2zfn1g5jmp19sj7l3na78nzzjgpf6q2q64r93igc", 5704 "depends": ["BiocManager", "GenomicRanges", "S4Vectors", "SummarizedExperiment"] 5705 }, 5706 "SeqSQC": { 5707 "name": "SeqSQC", 5708 "version": "1.32.0", 5709 "sha256": "0vx3xh0hk3yqv1fyimpwq04kvmzw6hqw8879f6ri3019vszl0apa", 5710 "depends": ["ExperimentHub", "GGally", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "SNPRelate", "e1071", "gdsfmt", "ggplot2", "plotly", "reshape2", "rmarkdown"] 5711 }, 5712 "SeqVarTools": { 5713 "name": "SeqVarTools", 5714 "version": "1.48.0", 5715 "sha256": "1ldvppx94wvahislg39hc3b4m45qdzpm8nbg2c77iv9w1b3411z8", 5716 "depends": ["Biobase", "BiocGenerics", "GWASExactHW", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SeqArray", "data_table", "gdsfmt", "logistf"] 5717 }, 5718 "Seqinfo": { 5719 "name": "Seqinfo", 5720 "version": "1.0.0", 5721 "sha256": "10jd4f4qvk4f2z4x9x6663fanh1mb0sxk9xs8giwbw1yb6jrab6p", 5722 "depends": ["BiocGenerics", "IRanges", "S4Vectors"] 5723 }, 5724 "SharedObject": { 5725 "name": "SharedObject", 5726 "version": "1.24.0", 5727 "sha256": "0wlhhnvy9hr9z6xsd24pz3y8yw32y4nmv0dn25rfcsai2a2wd7vp", 5728 "depends": ["BH", "BiocGenerics", "Rcpp"] 5729 }, 5730 "ShortRead": { 5731 "name": "ShortRead", 5732 "version": "1.68.0", 5733 "sha256": "16vjfqsj5mjzq8sh8px6qkcq6d9r95vnp77cgqxm80gqrqny9bj2", 5734 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicAlignments", "GenomicRanges", "IRanges", "Rhtslib", "Rsamtools", "S4Vectors", "Seqinfo", "XVector", "hwriter", "lattice", "latticeExtra", "pwalign"] 5735 }, 5736 "SiPSiC": { 5737 "name": "SiPSiC", 5738 "version": "1.10.0", 5739 "sha256": "1mm1a65vb51fzfziyia8dijlrinhlf8p1mvk0cvjh8pvdd6rjcm3", 5740 "depends": ["Matrix", "SingleCellExperiment"] 5741 }, 5742 "SigCheck": { 5743 "name": "SigCheck", 5744 "version": "2.42.0", 5745 "sha256": "01cz1xdb7fmlvky67jj1msmyjphc85qahh29rrai36xckbmy6rka", 5746 "depends": ["Biobase", "BiocParallel", "MLInterfaces", "e1071", "survival"] 5747 }, 5748 "SigsPack": { 5749 "name": "SigsPack", 5750 "version": "1.24.0", 5751 "sha256": "0j6lxlrvphhhm05dh1h7b48dqjrshalf81icdb3b0ggdqvymkrxz", 5752 "depends": ["BSgenome", "Biobase", "Biostrings", "GenomeInfoDb", "GenomicRanges", "SummarizedExperiment", "VariantAnnotation", "quadprog", "rtracklayer"] 5753 }, 5754 "SimBu": { 5755 "name": "SimBu", 5756 "version": "1.12.0", 5757 "sha256": "1cp4w554pmlq4kgbpaimdgk7gg7qwwfkcihawg1lg2nyb7l00sfj", 5758 "depends": ["BiocParallel", "Matrix", "RColorBrewer", "RCurl", "SummarizedExperiment", "basilisk", "data_table", "dplyr", "ggplot2", "phyloseq", "proxyC", "reticulate", "sparseMatrixStats", "tidyr"] 5759 }, 5760 "SimFFPE": { 5761 "name": "SimFFPE", 5762 "version": "1.22.0", 5763 "sha256": "139vs9n9ybps7i2gcs5q5vh18njifaz2xc50nrj30s7pspxyiib5", 5764 "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "doParallel", "dplyr", "foreach", "truncnorm"] 5765 }, 5766 "SingleCellAlleleExperiment": { 5767 "name": "SingleCellAlleleExperiment", 5768 "version": "1.6.0", 5769 "sha256": "1il9xdp8vv0sa9cdssv8n34knpiyqbixcmxnf048c576z9pyvzjb", 5770 "depends": ["BiocParallel", "DelayedArray", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment"] 5771 }, 5772 "SingleCellExperiment": { 5773 "name": "SingleCellExperiment", 5774 "version": "1.32.0", 5775 "sha256": "0a8p3i9zhgzl6lmms1l4nndjgm8czzjp70gj7q13zh26cb3hiyg3", 5776 "depends": ["BiocGenerics", "DelayedArray", "GenomicRanges", "S4Vectors", "SummarizedExperiment"] 5777 }, 5778 "SingleCellSignalR": { 5779 "name": "SingleCellSignalR", 5780 "version": "2.0.0", 5781 "sha256": "0pxpa1af6d6rkc33yxbal9g6lv9r4h2ikkwlvmlm0cznb6n466mc", 5782 "depends": ["BulkSignalR", "foreach", "ggplot2", "matrixStats", "matrixTests"] 5783 }, 5784 "SingleMoleculeFootprinting": { 5785 "name": "SingleMoleculeFootprinting", 5786 "version": "2.4.0", 5787 "sha256": "1gxk7msqac2qq0m9p4hr9gvxvz8gilz1cn3g4vca49mslxcjlhpy", 5788 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "Matrix", "QuasR", "RColorBrewer", "S4Vectors", "Seqinfo", "cluster", "dplyr", "ggplot2", "ggpointdensity", "ggrepel", "magrittr", "miscTools", "parallelDist", "patchwork", "plyranges", "qs", "rlang", "stringr", "tibble", "tidyr", "viridis"] 5789 }, 5790 "SingleR": { 5791 "name": "SingleR", 5792 "version": "2.12.0", 5793 "sha256": "0f7bfvyff044sf5dbgv3pfprl9qlgi16h737pfb0kq643s8ml45p", 5794 "depends": ["BiocNeighbors", "BiocParallel", "DelayedArray", "DelayedMatrixStats", "Matrix", "Rcpp", "S4Vectors", "SummarizedExperiment", "assorthead", "beachmat"] 5795 }, 5796 "Site2Target": { 5797 "name": "Site2Target", 5798 "version": "1.2.0", 5799 "sha256": "06nyf7vg22nhw2qk65ywl2za1850kjh1w7d9s55j7zk91fgfy93d", 5800 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "S4Vectors"] 5801 }, 5802 "SmartPhos": { 5803 "name": "SmartPhos", 5804 "version": "1.0.0", 5805 "sha256": "15ixzx0ps69wnyz51d492lyxca5rklrp82l8g0wf7k72h3jah8kj", 5806 "depends": ["Biobase", "BiocParallel", "DT", "MsCoreUtils", "MultiAssayExperiment", "SummarizedExperiment", "XML", "cowplot", "data_table", "decoupleR", "doParallel", "doRNG", "dplyr", "e1071", "factoextra", "ggbeeswarm", "ggplot2", "imputeLCMD", "limma", "magrittr", "matrixStats", "missForest", "pheatmap", "piano", "plotly", "proDA", "rlang", "shiny", "shinyBS", "shinyWidgets", "shinyjs", "shinythemes", "stringr", "tibble", "tidyr", "vsn"] 5807 }, 5808 "SomaticSignatures": { 5809 "name": "SomaticSignatures", 5810 "version": "2.46.0", 5811 "sha256": "1y6fcipzwnik016r6zllyi8ki9nqaz8hbx68rya5wdg16x3vngfp", 5812 "depends": ["Biobase", "Biostrings", "GenomicRanges", "IRanges", "NMF", "S4Vectors", "Seqinfo", "VariantAnnotation", "ggbio", "ggplot2", "pcaMethods", "proxy", "reshape2"] 5813 }, 5814 "SpaNorm": { 5815 "name": "SpaNorm", 5816 "version": "1.4.0", 5817 "sha256": "0g4899p805scvgjqar5fyqrxc0ysah83gi6waaz482hdlcdxkyp7", 5818 "depends": ["Matrix", "S4Vectors", "SeuratObject", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "edgeR", "ggplot2", "matrixStats", "rlang", "scran"] 5819 }, 5820 "SpaceMarkers": { 5821 "name": "SpaceMarkers", 5822 "version": "2.0.0", 5823 "sha256": "0xq2scbk6xb87r7zl93f62rl90f9wvypn9mda2c88qkzlv76m20i", 5824 "depends": ["Matrix", "RColorBrewer", "ape", "circlize", "dplyr", "effsize", "ggplot2", "hdf5r", "jsonlite", "matrixStats", "matrixTests", "mixtools", "nanoparquet", "qvalue", "readbitmap", "reshape2", "rlang", "rstatix", "spatstat_explore", "spatstat_geom", "viridis"] 5825 }, 5826 "SpaceTrooper": { 5827 "name": "SpaceTrooper", 5828 "version": "1.0.0", 5829 "sha256": "1xi8vzy975j6m7vgh9hxc5ifl6sj5m39fnaj4l8hxxqwxac7gkl5", 5830 "depends": ["DropletUtils", "S4Vectors", "SpatialExperiment", "SpatialExperimentIO", "SummarizedExperiment", "arrow", "cowplot", "data_table", "dplyr", "e1071", "ggplot2", "ggpubr", "glmnet", "rhdf5", "rlang", "robustbase", "scater", "scuttle", "sf", "sfheaders"] 5831 }, 5832 "Spaniel": { 5833 "name": "Spaniel", 5834 "version": "1.24.0", 5835 "sha256": "0vrhfmfgqs3am9d1c9mnl1nprpg25pgv5g54whpf11zd16vy9p0c", 5836 "depends": ["DropletUtils", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "igraph", "jpeg", "jsonlite", "magrittr", "png", "scater", "scran", "shiny"] 5837 }, 5838 "SparseArray": { 5839 "name": "SparseArray", 5840 "version": "1.10.0", 5841 "sha256": "1pywjz9pgy30iph6nq7nwdpqm6q980hxrb9qhz9c4ba9kgwk4pb6", 5842 "depends": ["BiocGenerics", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors", "XVector", "matrixStats"] 5843 }, 5844 "SparseSignatures": { 5845 "name": "SparseSignatures", 5846 "version": "2.20.0", 5847 "sha256": "1vy8gj0walh890rxj0hi84331i7gzkvk5dhafdg5mk7czmx4r80l", 5848 "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "NMF", "RhpcBLASctl", "data_table", "ggplot2", "gridExtra", "nnlasso", "nnls", "reshape2"] 5849 }, 5850 "SpatialCPie": { 5851 "name": "SpatialCPie", 5852 "version": "1.26.0", 5853 "sha256": "08lyfgvdm585c2xc0k5mlfpmf2zndrvjs6im277zf7nl5rcg2mly", 5854 "depends": ["SummarizedExperiment", "colorspace", "data_table", "digest", "dplyr", "ggforce", "ggiraph", "ggplot2", "ggrepel", "igraph", "lpSolve", "purrr", "readr", "rlang", "shiny", "shinyWidgets", "shinycssloaders", "shinyjs", "tibble", "tidyr", "tidyselect", "zeallot"] 5855 }, 5856 "SpatialDecon": { 5857 "name": "SpatialDecon", 5858 "version": "1.20.0", 5859 "sha256": "0y5wn3vi5a50c3745qxspxq89xj4j3bb0f2sj193j5qnyycli4px", 5860 "depends": ["Biobase", "GeomxTools", "Matrix", "SeuratObject", "logNormReg", "repmis"] 5861 }, 5862 "SpatialExperiment": { 5863 "name": "SpatialExperiment", 5864 "version": "1.20.0", 5865 "sha256": "1gnascjas2gz4h40gh9s1vf33cy6r85zq6l7lc8a2d9ifyp0pm0c", 5866 "depends": ["BiocFileCache", "BiocGenerics", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "magick", "rjson"] 5867 }, 5868 "SpatialExperimentIO": { 5869 "name": "SpatialExperimentIO", 5870 "version": "1.2.0", 5871 "sha256": "1gffisk37lr1awxymjwa6k0wcsd6clfpnkswrgsr2z5j2ifw04ky", 5872 "depends": ["DropletUtils", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "arrow", "data_table", "purrr"] 5873 }, 5874 "SpatialFeatureExperiment": { 5875 "name": "SpatialFeatureExperiment", 5876 "version": "1.11.1", 5877 "sha256": "0ps7fnjykpk630f6sffdavidg76rnjdwmcs759lvq0c17b3gscsr", 5878 "depends": ["Biobase", "BiocGenerics", "BiocNeighbors", "BiocParallel", "DropletUtils", "EBImage", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "data_table", "lifecycle", "rjson", "rlang", "sf", "sfheaders", "spatialreg", "spdep", "terra", "zeallot"] 5879 }, 5880 "SpatialOmicsOverlay": { 5881 "name": "SpatialOmicsOverlay", 5882 "version": "1.10.0", 5883 "sha256": "0bqgyfq67d87zdrplgqjzk9dj33ha3g6hzhar7g031wqxgas38r2", 5884 "depends": ["Biobase", "BiocFileCache", "EBImage", "GeomxTools", "RBioFormats", "S4Vectors", "XML", "base64enc", "data_table", "dplyr", "ggplot2", "ggtext", "magick", "pbapply", "plotrix", "readxl", "scattermore", "stringr"] 5885 }, 5886 "SpeCond": { 5887 "name": "SpeCond", 5888 "version": "1.64.0", 5889 "sha256": "088lwcy7qgbsr311r31fqyhvx13y7x2kr416z6c7kylh1l3qlbfb", 5890 "depends": ["Biobase", "RColorBrewer", "fields", "hwriter", "mclust"] 5891 }, 5892 "Spectra": { 5893 "name": "Spectra", 5894 "version": "1.20.0", 5895 "sha256": "0ajaxgsvg6aav2l74zmar76pwbjnrzd5sv8xv20v3jdcnwq33ghw", 5896 "depends": ["BiocGenerics", "BiocParallel", "IRanges", "MetaboCoreUtils", "MsCoreUtils", "ProtGenerics", "S4Vectors", "fs"] 5897 }, 5898 "SpectraQL": { 5899 "name": "SpectraQL", 5900 "version": "1.4.0", 5901 "sha256": "1md9sdqh9f5wca54a47nfj7lhcv6gf0z0g5xhfchqrzb88ldr5g1", 5902 "depends": ["MsCoreUtils", "ProtGenerics", "Spectra"] 5903 }, 5904 "SpectralTAD": { 5905 "name": "SpectralTAD", 5906 "version": "1.26.0", 5907 "sha256": "0l07d7hyamcjias3gcgb0gkgbrf8ha7d7lmzp3k121vydsg1drqa", 5908 "depends": ["BiocParallel", "GenomicRanges", "HiCcompare", "Matrix", "PRIMME", "cluster", "dplyr", "magrittr"] 5909 }, 5910 "SpectriPy": { 5911 "name": "SpectriPy", 5912 "version": "1.0.0", 5913 "sha256": "0k96x0nijgw01d0x0irbnj1ia0i046zbndf4j7fhk4fqpc79qakl", 5914 "depends": ["IRanges", "MsCoreUtils", "ProtGenerics", "S4Vectors", "Spectra", "reticulate"] 5915 }, 5916 "SpliceWiz": { 5917 "name": "SpliceWiz", 5918 "version": "1.12.0", 5919 "sha256": "02g7h7yaqkallwalx57w9hli02xzar2bcvqv06sx63jpfaar34xv", 5920 "depends": ["AnnotationHub", "BSgenome", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "DT", "DelayedArray", "DelayedMatrixStats", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "NxtIRFdata", "RColorBrewer", "RSQLite", "R_utils", "Rcpp", "RcppProgress", "S4Vectors", "SummarizedExperiment", "data_table", "fst", "genefilter", "ggplot2", "h5mread", "heatmaply", "htmltools", "httr", "magrittr", "matrixStats", "ompBAM", "patchwork", "pheatmap", "plotly", "progress", "rhandsontable", "rhdf5", "rtracklayer", "rvest", "scales", "shiny", "shinyFiles", "shinyWidgets", "shinydashboard", "stringi"] 5921 }, 5922 "SplicingFactory": { 5923 "name": "SplicingFactory", 5924 "version": "1.18.0", 5925 "sha256": "12iswmi8mzz3kbbjr2lf02p35gvbzds588i59msyw4803vravdlh", 5926 "depends": ["SummarizedExperiment"] 5927 }, 5928 "SplicingGraphs": { 5929 "name": "SplicingGraphs", 5930 "version": "1.49.1", 5931 "sha256": "1bi722gg24lv2rljps4gpkaqa560z39q76wzqf03zp08616fgfkm", 5932 "depends": ["BiocGenerics", "BiocParallel", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rgraphviz", "Rsamtools", "S4Vectors", "Seqinfo", "graph", "igraph"] 5933 }, 5934 "SplineDV": { 5935 "name": "SplineDV", 5936 "version": "1.2.0", 5937 "sha256": "0nf35ljh2hrh05x3a5fj273ibd7knm390li6na5maq763vyvx4zb", 5938 "depends": ["Biobase", "BiocGenerics", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "plotly", "scuttle", "sparseMatrixStats"] 5939 }, 5940 "SpotClean": { 5941 "name": "SpotClean", 5942 "version": "1.12.0", 5943 "sha256": "0y4cbv5hcz9q4wcgx4hr66998bpzxlsdlgski2wca6ag604ryxjy", 5944 "depends": ["Matrix", "RColorBrewer", "S4Vectors", "Seurat", "SpatialExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "readbitmap", "rhdf5", "rjson", "rlang", "tibble", "viridis"] 5945 }, 5946 "SpotSweeper": { 5947 "name": "SpotSweeper", 5948 "version": "1.6.0", 5949 "sha256": "16f6dqafv7lps5k5lnjzd612fcgkhlpl13l89p5036qxmfhwxvmi", 5950 "depends": ["BiocNeighbors", "BiocParallel", "MASS", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "escheR", "ggplot2", "spatialEco"] 5951 }, 5952 "StabMap": { 5953 "name": "StabMap", 5954 "version": "1.4.0", 5955 "sha256": "0pqk8i63w1x3ksjfygyf819gr93yb3jl5kpdvwz04r16n3n3sxaq", 5956 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "MASS", "Matrix", "MatrixGenerics", "SummarizedExperiment", "abind", "igraph", "slam"] 5957 }, 5958 "Statial": { 5959 "name": "Statial", 5960 "version": "1.12.0", 5961 "sha256": "10apydvjfj7jlg5ns55rfy4zsy99lzwzc7bxjn8h3aygs9nwnv60", 5962 "depends": ["BiocParallel", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cluster", "concaveman", "data_table", "dplyr", "edgeR", "ggplot2", "limma", "magrittr", "plotly", "purrr", "ranger", "spatstat_explore", "spatstat_geom", "stringr", "tibble", "tidyr", "tidyselect", "treekoR"] 5963 }, 5964 "Streamer": { 5965 "name": "Streamer", 5966 "version": "1.56.0", 5967 "sha256": "0sg7as0b12d0lwh2wavvb036v55dzf8y8xixa6q75hrs2zw0x47w", 5968 "depends": ["BiocGenerics", "RBGL", "graph"] 5969 }, 5970 "Structstrings": { 5971 "name": "Structstrings", 5972 "version": "1.26.0", 5973 "sha256": "0lmymq8lgaiw8v8l1fln728yb4iky6ypslw7hn5lg48w9fjhgiqv", 5974 "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors", "XVector", "crayon", "stringi", "stringr"] 5975 }, 5976 "StructuralVariantAnnotation": { 5977 "name": "StructuralVariantAnnotation", 5978 "version": "1.26.0", 5979 "sha256": "0lqk2fwpz3nkz5ww4lcz6751hjkcmc2wgdxk07fb56qkzbpyg5f8", 5980 "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "assertthat", "dplyr", "pwalign", "rlang", "rtracklayer", "stringr"] 5981 }, 5982 "SubCellBarCode": { 5983 "name": "SubCellBarCode", 5984 "version": "1.26.0", 5985 "sha256": "1c20fnjzqfsbj2ay6cm0401yv4v0a7s61cvzl1y95drh5r6g0y5h", 5986 "depends": ["AnnotationDbi", "Rtsne", "caret", "e1071", "ggplot2", "ggrepel", "gridExtra", "networkD3", "org_Hs_eg_db", "scatterplot3d"] 5987 }, 5988 "SummarizedExperiment": { 5989 "name": "SummarizedExperiment", 5990 "version": "1.40.0", 5991 "sha256": "1xmlfrdhzlbsd23warfdm5iscm61r29jxridv8krv16b95l4axk9", 5992 "depends": ["Biobase", "BiocGenerics", "DelayedArray", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "S4Arrays", "S4Vectors", "Seqinfo"] 5993 }, 5994 "Summix": { 5995 "name": "Summix", 5996 "version": "2.16.0", 5997 "sha256": "1sy7gi33zzd1wv5ql16r6qjmqlhxgkdkbbvjzkxdxpr0dq8k18l6", 5998 "depends": ["BEDASSLE", "dplyr", "magrittr", "nloptr", "randomcoloR", "scales", "tibble", "tidyselect", "visNetwork"] 5999 }, 6000 "SuperCellCyto": { 6001 "name": "SuperCellCyto", 6002 "version": "1.0.0", 6003 "sha256": "0l4ajfp4gjfkpry31aiwsy1x8wwg87aq5zj52szhn982xfrzjya1", 6004 "depends": ["BiocParallel", "Matrix", "SuperCell", "data_table"] 6005 }, 6006 "SurfR": { 6007 "name": "SurfR", 6008 "version": "1.6.0", 6009 "sha256": "19kzdq6h56wmc1fryb7zhsa14d9cyqlhf5pgk653jz69iy0z72m1", 6010 "depends": ["BiocFileCache", "DESeq2", "SPsimSeq", "SummarizedExperiment", "TCGAbiolinks", "assertr", "biomaRt", "curl", "dplyr", "edgeR", "ggplot2", "ggrepel", "gridExtra", "httr", "knitr", "magrittr", "metaRNASeq", "openxlsx", "rhdf5", "rjson", "scales", "stringr", "tidyr", "venn"] 6011 }, 6012 "SwathXtend": { 6013 "name": "SwathXtend", 6014 "version": "2.32.0", 6015 "sha256": "1149rnh1h71afza6a0xjjgjgn10afdsc6vsqsvj7n6pb8lannzxy", 6016 "depends": ["VennDiagram", "e1071", "lattice", "openxlsx"] 6017 }, 6018 "SynExtend": { 6019 "name": "SynExtend", 6020 "version": "1.22.0", 6021 "sha256": "14j98vhbm3hh2d995za5mkjrr37gwfvrigwyj1ybg9bvvqfkf6mq", 6022 "depends": ["Biostrings", "DBI", "DECIPHER", "IRanges", "RSQLite", "S4Vectors"] 6023 }, 6024 "SynMut": { 6025 "name": "SynMut", 6026 "version": "1.26.0", 6027 "sha256": "0zi4zlnnayb026rfra2d5lw5l1slp70s6lblvwsj3gszivgcvc7b", 6028 "depends": ["BiocGenerics", "Biostrings", "seqinr", "stringr"] 6029 }, 6030 "TADCompare": { 6031 "name": "TADCompare", 6032 "version": "1.20.0", 6033 "sha256": "0gwcc4rld9jm7wrq2dfg9fa1qvfb6v48ldcinfjzkjf2whj3kcn9", 6034 "depends": ["HiCcompare", "Matrix", "PRIMME", "RColorBrewer", "cluster", "cowplot", "dplyr", "ggplot2", "ggpubr", "magrittr", "reshape2", "tidyr"] 6035 }, 6036 "TAPseq": { 6037 "name": "TAPseq", 6038 "version": "1.22.0", 6039 "sha256": "0djj1sz0ml831rgv974277i65lrghv1a2xc8jjjd0cs5xzci97ri", 6040 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "dplyr", "tidyr"] 6041 }, 6042 "TBSignatureProfiler": { 6043 "name": "TBSignatureProfiler", 6044 "version": "1.22.0", 6045 "sha256": "0ilp68m46qdh45rzksmbvnykvbwbpw75gww66n0glga4pkp551xk", 6046 "depends": ["ASSIGN", "BiocParallel", "ComplexHeatmap", "DESeq2", "DT", "GSVA", "HGNChelper", "RColorBrewer", "ROCit", "S4Vectors", "SummarizedExperiment", "edgeR", "gdata", "ggplot2", "glmnet", "magrittr", "pROC", "reshape2", "singscore", "tibble"] 6047 }, 6048 "TCC": { 6049 "name": "TCC", 6050 "version": "1.50.0", 6051 "sha256": "14hbv28nrg81n905c5g0gmrl3qycwqn6mi2cbvc4cnhymzvcw20f", 6052 "depends": ["DESeq2", "ROC", "edgeR"] 6053 }, 6054 "TCGAbiolinks": { 6055 "name": "TCGAbiolinks", 6056 "version": "2.38.0", 6057 "sha256": "1ysxy8jc06szqysw54j8hznc2vy0w3m1cr822cy6g4pfbdsqflp9", 6058 "depends": ["GenomicRanges", "IRanges", "R_utils", "S4Vectors", "SummarizedExperiment", "TCGAbiolinksGUI_data", "XML", "biomaRt", "data_table", "downloader", "dplyr", "ggplot2", "httr", "jsonlite", "knitr", "plyr", "purrr", "readr", "rvest", "stringr", "tibble", "tidyr", "xml2"] 6059 }, 6060 "TCGAutils": { 6061 "name": "TCGAutils", 6062 "version": "1.29.5", 6063 "sha256": "051ylfrkbf0dx2m47hqbm4d0sw47nwmlhzwzalyx4j484jn4kra2", 6064 "depends": ["AnnotationDbi", "BiocBaseUtils", "BiocGenerics", "GenomeInfoDb", "GenomicDataCommons", "GenomicFeatures", "GenomicRanges", "IRanges", "MultiAssayExperiment", "RaggedExperiment", "S4Vectors", "Seqinfo", "SummarizedExperiment", "rvest", "stringr", "xml2"] 6065 }, 6066 "TCseq": { 6067 "name": "TCseq", 6068 "version": "1.34.0", 6069 "sha256": "156k83g75i2ndi7gc0li2zngad4s9bqn4ygi9lj5mlnf2lhr0rlq", 6070 "depends": ["BiocGenerics", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "cluster", "e1071", "edgeR", "ggplot2", "locfit", "reshape2"] 6071 }, 6072 "TDbasedUFE": { 6073 "name": "TDbasedUFE", 6074 "version": "1.10.0", 6075 "sha256": "1d130jjazb21x93cw000z22hs9iic5l47sw7z38jv42pq7xv4xfa", 6076 "depends": ["GenomicRanges", "MOFAdata", "rTensor", "readr", "shiny", "tximport", "tximportData"] 6077 }, 6078 "TDbasedUFEadv": { 6079 "name": "TDbasedUFEadv", 6080 "version": "1.10.0", 6081 "sha256": "0wqi3rdiyhl7sxccwqcmnyzl5yfd3c4f4nliksbmja7xm5frm4hq", 6082 "depends": ["Biobase", "DOSE", "GenomicRanges", "RTCGA", "STRINGdb", "TDbasedUFE", "enrichR", "enrichplot", "hash", "rTensor", "shiny"] 6083 }, 6084 "TEKRABber": { 6085 "name": "TEKRABber", 6086 "version": "1.14.0", 6087 "sha256": "13cqkkqhcwx9gygkkqjgjb3iph8q38nwx637dadk69gbqbslkm0g", 6088 "depends": ["DESeq2", "Rcpp", "SCBN", "Seqinfo", "apeglm", "biomaRt", "doParallel", "dplyr", "foreach", "magrittr", "rtracklayer"] 6089 }, 6090 "TENET": { 6091 "name": "TENET", 6092 "version": "1.2.0", 6093 "sha256": "1s5cb3lyy22p69x2vkd1igbn7limhkfchfk3dwg3fvkbxk299xdv", 6094 "depends": ["AnnotationHub", "BAMMtools", "BSgenome_Hsapiens_UCSC_hg38", "Biostrings", "ExperimentHub", "GenomicRanges", "IRanges", "MotifDb", "MultiAssayExperiment", "RCircos", "R_utils", "S4Vectors", "SummarizedExperiment", "TCGAbiolinks", "TENET_ExperimentHub", "ggplot2", "matlab", "pastecs", "rtracklayer", "seqLogo", "sesame", "sesameData", "survival", "survminer"] 6095 }, 6096 "TENxIO": { 6097 "name": "TENxIO", 6098 "version": "1.12.0", 6099 "sha256": "1vwp8cqvlz0d4bid7wwv3xrn2mg4920sraz41m55b1riawqdnxdp", 6100 "depends": ["BiocBaseUtils", "BiocGenerics", "BiocIO", "GenomicRanges", "HDF5Array", "Matrix", "MatrixGenerics", "RCurl", "R_utils", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SummarizedExperiment", "readr", "rhdf5"] 6101 }, 6102 "TEQC": { 6103 "name": "TEQC", 6104 "version": "4.32.0", 6105 "sha256": "1kh9h2lw0lg9qafxqv78wm5j5jc138zqr9raizpa7czvwg7ppc7b", 6106 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "hwriter"] 6107 }, 6108 "TFARM": { 6109 "name": "TFARM", 6110 "version": "1.32.0", 6111 "sha256": "16izz3krw786k3ryf1zs6lhi9kdx0w1cwfcawcp0rzwwwhn8x7nm", 6112 "depends": ["GenomicRanges", "arules", "fields", "gplots", "stringr"] 6113 }, 6114 "TFBSTools": { 6115 "name": "TFBSTools", 6116 "version": "1.48.0", 6117 "sha256": "0vsl5i3nv57ha47qa5ba3sd99n9sd6px402wqr80fv9636qb85nq", 6118 "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DBI", "DirichletMultinomial", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "Seqinfo", "TFMPvalue", "XML", "XVector", "caTools", "gtools", "pwalign", "rtracklayer", "seqLogo"] 6119 }, 6120 "TFEA_ChIP": { 6121 "name": "TFEA.ChIP", 6122 "version": "1.30.0", 6123 "sha256": "0cyd9qghhvan8gb8dgdcsglmi2c73axd50sd3g9bjzj7rxwpks36", 6124 "depends": ["ExperimentHub", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "biomaRt", "dplyr", "org_Hs_eg_db", "org_Mm_eg_db", "rlang"] 6125 }, 6126 "TFHAZ": { 6127 "name": "TFHAZ", 6128 "version": "1.32.0", 6129 "sha256": "0fp26qlcq6yasj4m7zc05lvj2x45waj0w0862976m756z55ximzb", 6130 "depends": ["GenomicRanges", "IRanges", "ORFik", "S4Vectors"] 6131 }, 6132 "TFutils": { 6133 "name": "TFutils", 6134 "version": "1.30.0", 6135 "sha256": "14ks561m1n3jq96x51x3127nr5gjndvkcjvk1xrp2ccifdniwl29", 6136 "depends": ["AnnotationDbi", "BiocFileCache", "DT", "GSEABase", "GenomicFiles", "Rsamtools", "SummarizedExperiment", "dplyr", "httr", "magrittr", "miniUI", "org_Hs_eg_db", "readxl", "rjson", "shiny"] 6137 }, 6138 "TIN": { 6139 "name": "TIN", 6140 "version": "1.42.0", 6141 "sha256": "1zzglfmipsabf3zbphv0dcjgzb2lwyksg728nvc8k2s2q2y6cbyk", 6142 "depends": ["WGCNA", "aroma_affymetrix", "data_table", "impute", "squash", "stringr"] 6143 }, 6144 "TMSig": { 6145 "name": "TMSig", 6146 "version": "1.4.0", 6147 "sha256": "01hzm0b7qyyr666yhk6lb2yv130pjs0ar5ss7jphqshr16h6m0mc", 6148 "depends": ["ComplexHeatmap", "GSEABase", "Matrix", "circlize", "data_table", "limma"] 6149 }, 6150 "TMixClust": { 6151 "name": "TMixClust", 6152 "version": "1.32.0", 6153 "sha256": "0ards0ri8g82ianzdidm6bdh64j4jljag8lw9dyilh9d5kqabciz", 6154 "depends": ["Biobase", "BiocParallel", "SPEM", "cluster", "flexclust", "gss", "mvtnorm", "zoo"] 6155 }, 6156 "TOAST": { 6157 "name": "TOAST", 6158 "version": "1.24.0", 6159 "sha256": "1cmi1avi7ypy20r0vqyid72zfsas8ch4b2li6s9h9acbi98flzz9", 6160 "depends": ["EpiDISH", "GGally", "SummarizedExperiment", "corpcor", "doParallel", "ggplot2", "limma", "nnls", "quadprog", "tidyr"] 6161 }, 6162 "TOP": { 6163 "name": "TOP", 6164 "version": "1.10.0", 6165 "sha256": "152yyajddx7sxigky8s4pymsfrmabiiib4rfvpm3n8pb0mp5if2x", 6166 "depends": ["ClassifyR", "Hmisc", "assertthat", "caret", "directPA", "doParallel", "dplyr", "ggnewscale", "ggplot2", "ggraph", "ggrepel", "ggthemes", "glmnet", "igraph", "latex2exp", "limma", "magrittr", "pROC", "plotly", "purrr", "reshape2", "statmod", "stringr", "survival", "tibble", "tidygraph", "tidyr"] 6167 }, 6168 "TPP": { 6169 "name": "TPP", 6170 "version": "3.38.0", 6171 "sha256": "043y7vjr2g62vqky6k7zr262vza5lswrapx0hx2jq9sh4xibizh9", 6172 "depends": ["Biobase", "MASS", "RColorBrewer", "RCurl", "VGAM", "VennDiagram", "biobroom", "broom", "data_table", "doParallel", "dplyr", "foreach", "futile_logger", "ggplot2", "gridExtra", "knitr", "limma", "magrittr", "mefa", "nls2", "openxlsx", "plyr", "purrr", "reshape2", "rmarkdown", "stringr", "tibble", "tidyr"] 6173 }, 6174 "TPP2D": { 6175 "name": "TPP2D", 6176 "version": "1.26.0", 6177 "sha256": "117avbbvnvnji5nlk8figs4j2ih9ylfy0k1ryvqv4b9gjg6hqhbn", 6178 "depends": ["BiocParallel", "MASS", "RCurl", "doParallel", "dplyr", "foreach", "ggplot2", "limma", "openxlsx", "stringr", "tidyr"] 6179 }, 6180 "TREG": { 6181 "name": "TREG", 6182 "version": "1.14.0", 6183 "sha256": "1c460crq072651h5156qb1wqraljnwhwm8bjy7d4gv8i57dbl6vx", 6184 "depends": ["Matrix", "SummarizedExperiment", "purrr", "rafalib"] 6185 }, 6186 "TRESS": { 6187 "name": "TRESS", 6188 "version": "1.16.0", 6189 "sha256": "0xn1lgjb44vxfcwimq06dvj997ianr60nydfawl3pjjxpa7yfmi9", 6190 "depends": ["AnnotationDbi", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rsamtools", "S4Vectors", "matrixStats", "rtracklayer"] 6191 }, 6192 "TRONCO": { 6193 "name": "TRONCO", 6194 "version": "2.42.0", 6195 "sha256": "0fwvyazzbfjjdivpgml5jjb9r0k07kapkrl4jif1m4mfz24icc9i", 6196 "depends": ["RColorBrewer", "R_matlab", "Rgraphviz", "bnlearn", "circlize", "doParallel", "foreach", "gridExtra", "gtable", "gtools", "igraph", "iterators", "scales", "xtable"] 6197 }, 6198 "TSAR": { 6199 "name": "TSAR", 6200 "version": "1.8.0", 6201 "sha256": "1bbrqx70hzjxcfr0pgvqxc6yas51qkqzarmncgpqc7b0cpwiv50i", 6202 "depends": ["dplyr", "ggplot2", "ggpubr", "jsonlite", "magrittr", "mgcv", "minpack_lm", "openxlsx", "plotly", "readxl", "rhandsontable", "shiny", "shinyWidgets", "shinyjs", "stringr", "tidyr"] 6203 }, 6204 "TSCAN": { 6205 "name": "TSCAN", 6206 "version": "1.48.0", 6207 "sha256": "14r33cyiy80pksbiwx7hnmxlhimvxhzw2vnvilx4hk90qypda9xk", 6208 "depends": ["DelayedArray", "Matrix", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "TrajectoryUtils", "combinat", "fastICA", "ggplot2", "gplots", "igraph", "mclust", "mgcv", "plyr", "shiny"] 6209 }, 6210 "TTMap": { 6211 "name": "TTMap", 6212 "version": "1.32.0", 6213 "sha256": "0pz3h6ybckmfk6y7ajr1sk6yhybqxyhpmh65glfrvhf4rc1cpysc", 6214 "depends": ["Biobase", "SummarizedExperiment", "colorRamps", "rgl"] 6215 }, 6216 "TVTB": { 6217 "name": "TVTB", 6218 "version": "1.36.0", 6219 "sha256": "0v4mrcrdlncbi52mxl3pxa8w4p1v4ws6zmfin56c9kcsfrngwp6s", 6220 "depends": ["AnnotationFilter", "BiocGenerics", "BiocParallel", "Biostrings", "GGally", "GenomicRanges", "Gviz", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "ensembldb", "ggplot2", "limma", "reshape2"] 6221 }, 6222 "TargetDecoy": { 6223 "name": "TargetDecoy", 6224 "version": "1.16.0", 6225 "sha256": "0dcwnffgp6kmw62jfcnbw3shbb6gmsm4982yrmgrbwc0wddb6jgi", 6226 "depends": ["ggplot2", "ggpubr", "miniUI", "mzID", "mzR", "shiny"] 6227 }, 6228 "TargetScore": { 6229 "name": "TargetScore", 6230 "version": "1.48.0", 6231 "sha256": "0yrq8gmd62apl06m4ag3jdy0km8k0np2ijhda16xfk0y4kf4pdim", 6232 "depends": ["Matrix", "pracma"] 6233 }, 6234 "TargetSearch": { 6235 "name": "TargetSearch", 6236 "version": "2.12.0", 6237 "sha256": "0cshl6mdqwkndzh2295rf5msg4niysfy2d82xg5c3842vbjlp40r", 6238 "depends": ["assertthat", "ncdf4"] 6239 }, 6240 "TaxSEA": { 6241 "name": "TaxSEA", 6242 "version": "1.2.0", 6243 "sha256": "18dfz7pijpral6mzhx3vjm1gyf0d653jq9iypbs6z7p8g342wyyw", 6244 "depends": [] 6245 }, 6246 "TileDBArray": { 6247 "name": "TileDBArray", 6248 "version": "1.20.0", 6249 "sha256": "0czy2xn55zld91zqpj16cd3nnys1v0bh61kw408njslxgwslsnrz", 6250 "depends": ["DelayedArray", "S4Vectors", "SparseArray", "tiledb"] 6251 }, 6252 "TissueEnrich": { 6253 "name": "TissueEnrich", 6254 "version": "1.30.0", 6255 "sha256": "0ysk3wx7c73ljgz78ywkriirxlbpnwg1n3rv24qi24rh9n9j2n5f", 6256 "depends": ["GSEABase", "SummarizedExperiment", "dplyr", "ggplot2", "tidyr"] 6257 }, 6258 "TnT": { 6259 "name": "TnT", 6260 "version": "1.32.0", 6261 "sha256": "0f3q1g6zqcpxl5f1icj8frdlpmxwnf2lgrab7z1n6bssdvvjv5r2", 6262 "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "data_table", "htmlwidgets", "jsonlite", "knitr"] 6263 }, 6264 "ToxicoGx": { 6265 "name": "ToxicoGx", 6266 "version": "2.14.0", 6267 "sha256": "01y338mxf3sx3rkmzd5dnlk04x3nwbk15vnigjyhaq2h18gc5qqy", 6268 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "CoreGx", "S4Vectors", "SummarizedExperiment", "assertthat", "caTools", "data_table", "downloader", "dplyr", "ggplot2", "jsonlite", "limma", "magrittr", "reshape2", "scales", "tibble", "tidyr"] 6269 }, 6270 "TrIdent": { 6271 "name": "TrIdent", 6272 "version": "1.2.0", 6273 "sha256": "0ap55nnljg1q4d4vg1rz9k9d0fy5dx71ha26haw98kbb04jxbbps", 6274 "depends": ["dplyr", "ggplot2", "patchwork", "roll", "stringr", "tidyr"] 6275 }, 6276 "TrajectoryGeometry": { 6277 "name": "TrajectoryGeometry", 6278 "version": "1.18.0", 6279 "sha256": "12s9lq46admw4akfxpcgxkq6l46z02k00lx6q7h386p4lbr9f32k", 6280 "depends": ["ggplot2", "pracma", "rgl"] 6281 }, 6282 "TrajectoryUtils": { 6283 "name": "TrajectoryUtils", 6284 "version": "1.18.0", 6285 "sha256": "0y2d2pxsiagzzqplbwz6qmkcd3rqq77j6zsj8i987dwk13p5gy4f", 6286 "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "igraph"] 6287 }, 6288 "TreeAndLeaf": { 6289 "name": "TreeAndLeaf", 6290 "version": "1.22.0", 6291 "sha256": "0ql61a8a3wl1fp9wkliqk7794jhvgx062i1awy1k3aipwl9lwyay", 6292 "depends": ["RedeR", "ape", "igraph"] 6293 }, 6294 "TreeSummarizedExperiment": { 6295 "name": "TreeSummarizedExperiment", 6296 "version": "2.18.0", 6297 "sha256": "15kqkj3hz24mbiz9bs63frfl983f4vv1byki32g4fljhwd6xv0m9", 6298 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "IRanges", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ape", "dplyr", "rlang", "treeio"] 6299 }, 6300 "Trendy": { 6301 "name": "Trendy", 6302 "version": "1.32.0", 6303 "sha256": "0cyxb4xdfr52vynwjwysrnxd8xn386iy72yzg81d20v27yykd4yv", 6304 "depends": ["BiocParallel", "DT", "S4Vectors", "SummarizedExperiment", "gplots", "magrittr", "segmented", "shiny", "shinyFiles"] 6305 }, 6306 "TurboNorm": { 6307 "name": "TurboNorm", 6308 "version": "1.58.0", 6309 "sha256": "068g9q3111bshis8f0f236jhbpyy5nm1h203ibfllkq1pvw4l6cr", 6310 "depends": ["affy", "convert", "lattice", "limma", "marray"] 6311 }, 6312 "UCSC_utils": { 6313 "name": "UCSC.utils", 6314 "version": "1.6.0", 6315 "sha256": "0ylb4d3bsl859609b4wsclhhv2zrvhkcr25q5mv6ywyvppri3j1y", 6316 "depends": ["S4Vectors", "httr", "jsonlite"] 6317 }, 6318 "UCell": { 6319 "name": "UCell", 6320 "version": "2.14.0", 6321 "sha256": "06bznwjswqv7fz5m2pjhzzj70c14a6v44sdgwwg436g21znjxpyr", 6322 "depends": ["BiocNeighbors", "BiocParallel", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "data_table"] 6323 }, 6324 "UMI4Cats": { 6325 "name": "UMI4Cats", 6326 "version": "1.20.0", 6327 "sha256": "162f89h9jid1bqsym1mqaw7xfnax57na18ng5f815wf2r2x03a3i", 6328 "depends": ["BSgenome", "BiocFileCache", "BiocGenerics", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "R_utils", "Rbowtie2", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "annotate", "cowplot", "dplyr", "fda", "ggplot2", "magick", "rappdirs", "regioneR", "reshape2", "rlang", "scales", "stringr", "zoo"] 6329 }, 6330 "UNDO": { 6331 "name": "UNDO", 6332 "version": "1.52.0", 6333 "sha256": "1rkrfcl8l4p5pi3qqn0lzyr4l6a75qnp0sdj4hrz5rz72fsqn02y", 6334 "depends": ["Biobase", "BiocGenerics", "MASS", "boot", "nnls"] 6335 }, 6336 "UPDhmm": { 6337 "name": "UPDhmm", 6338 "version": "1.6.0", 6339 "sha256": "1rn1jijmpx7j165q210l76hyq3aj7ir02zh64cn85a04razs2qrx", 6340 "depends": ["Biobase", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "HMM", "IRanges", "S4Vectors", "SummarizedExperiment", "VariantAnnotation"] 6341 }, 6342 "Ularcirc": { 6343 "name": "Ularcirc", 6344 "version": "1.28.0", 6345 "sha256": "1k8x7g5fgssj01i8b60fyhsh09hmxj06k0ghxrk70jijp8y49906", 6346 "depends": ["AnnotationDbi", "AnnotationHub", "BSgenome", "BiocGenerics", "Biostrings", "DT", "GenomeInfoDb", "GenomeInfoDbData", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Organism_dplyr", "R_utils", "S4Vectors", "data_table", "ggplot2", "ggrepel", "gsubfn", "moments", "plotgardener", "shiny", "shinyFiles", "shinydashboard", "shinyjs", "yaml"] 6347 }, 6348 "UniProt_ws": { 6349 "name": "UniProt.ws", 6350 "version": "2.50.0", 6351 "sha256": "0jbn2ijcrpq942afn5gq5f4lqqzgbx4c2r7z0cn9kk69h7q695zv", 6352 "depends": ["AnnotationDbi", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "httr2", "jsonlite", "progress", "rjsoncons", "rlang"] 6353 }, 6354 "Uniquorn": { 6355 "name": "Uniquorn", 6356 "version": "2.30.0", 6357 "sha256": "1l068kjphna85z98xwqh4i4qxrvprl4wc8rp9lcgh692vhbsxjgb", 6358 "depends": ["GenomicRanges", "IRanges", "R_utils", "VariantAnnotation", "WriteXLS", "data_table", "doParallel", "foreach", "stringr"] 6359 }, 6360 "VAExprs": { 6361 "name": "VAExprs", 6362 "version": "1.16.0", 6363 "sha256": "0ypi6hhqlkv80fgpg36jfsm365ibljsj4h3nn6yqazigaisi7y4c", 6364 "depends": ["CatEncoders", "DeepPINCS", "DiagrammeR", "SingleCellExperiment", "SummarizedExperiment", "keras", "mclust", "purrr", "scater", "tensorflow"] 6365 }, 6366 "VCFArray": { 6367 "name": "VCFArray", 6368 "version": "1.26.0", 6369 "sha256": "1j0ckv4d7a6nzxc53sih30kdb3l4bbk6db53zkv0hz4bpdzq6mrw", 6370 "depends": ["BiocGenerics", "DelayedArray", "GenomicFiles", "GenomicRanges", "Rsamtools", "S4Vectors", "VariantAnnotation"] 6371 }, 6372 "VDJdive": { 6373 "name": "VDJdive", 6374 "version": "1.12.0", 6375 "sha256": "03vz55d7lpclrw059hp914ak5jrhbmc20kp1siylz2m2izbz7vyy", 6376 "depends": ["BiocParallel", "IRanges", "Matrix", "RColorBrewer", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cowplot", "ggplot2", "gridExtra"] 6377 }, 6378 "VERSO": { 6379 "name": "VERSO", 6380 "version": "1.20.0", 6381 "sha256": "0cg61j5cwp1i9xaj5hknwavjfzq14f1sqkw6zqbghb6bhl99xccx", 6382 "depends": ["Rfast", "ape", "data_tree"] 6383 }, 6384 "VaSP": { 6385 "name": "VaSP", 6386 "version": "1.22.0", 6387 "sha256": "0nmjic140biq4rfi7gq2kwh4vk7bicqwmkc4ww93c1lwl674znd0", 6388 "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ballgown", "cluster", "matrixStats"] 6389 }, 6390 "VanillaICE": { 6391 "name": "VanillaICE", 6392 "version": "1.72.0", 6393 "sha256": "0n7ir8r23pf9mazgrmyqyr8d1h1n7pm7p995p1ip0rq4cvbdmz96", 6394 "depends": ["BSgenome_Hsapiens_UCSC_hg18", "Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MatrixGenerics", "S4Vectors", "SummarizedExperiment", "crlmm", "data_table", "foreach", "lattice", "matrixStats", "oligoClasses"] 6395 }, 6396 "VarCon": { 6397 "name": "VarCon", 6398 "version": "1.18.0", 6399 "sha256": "0fancb3r8r8kdzg0668fdjjx08q9zr0hp94ssyiyi20jsvwia0cq", 6400 "depends": ["BSgenome", "Biostrings", "GenomicRanges", "IRanges", "ggplot2", "shiny", "shinyFiles", "shinycssloaders"] 6401 }, 6402 "VariantAnnotation": { 6403 "name": "VariantAnnotation", 6404 "version": "1.56.0", 6405 "sha256": "008saw81bnzdyglysqcbmp745k8pxgx3ng7hkpqdry773vf3xfn8", 6406 "depends": ["AnnotationDbi", "BSgenome", "Biobase", "BiocGenerics", "Biostrings", "DBI", "GenomicFeatures", "GenomicRanges", "IRanges", "MatrixGenerics", "Rhtslib", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "XVector", "curl", "rtracklayer"] 6407 }, 6408 "VariantExperiment": { 6409 "name": "VariantExperiment", 6410 "version": "1.24.0", 6411 "sha256": "12y7jafybsr74mjgfph87kxhj990bf9v795n3yj1mx4m2wiw211l", 6412 "depends": ["Biostrings", "DelayedArray", "DelayedDataFrame", "GDSArray", "GenomicRanges", "IRanges", "S4Vectors", "SNPRelate", "SeqArray", "SummarizedExperiment", "gdsfmt"] 6413 }, 6414 "VariantFiltering": { 6415 "name": "VariantFiltering", 6416 "version": "1.46.0", 6417 "sha256": "070n6iq21pzq2d146d5sh9yjbmpyw617bskyfbfkpz0dh2fhxbgz", 6418 "depends": ["AnnotationDbi", "BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DT", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "GenomicScores", "Gviz", "IRanges", "RBGL", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "XVector", "graph", "shiny", "shinyTree", "shinyjs", "shinythemes"] 6419 }, 6420 "VariantTools": { 6421 "name": "VariantTools", 6422 "version": "1.51.0", 6423 "sha256": "14r5hnc095v1h2q2bfsgqfmmmfzdnl5srac3xla1qjq9d8xv5m7v", 6424 "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rsamtools", "S4Vectors", "VariantAnnotation", "rtracklayer"] 6425 }, 6426 "VegaMC": { 6427 "name": "VegaMC", 6428 "version": "3.48.0", 6429 "sha256": "0b90r3960ghkqp12spj6hkm113r8bbpkl0j68w0mg2070dihdbh4", 6430 "depends": ["Biobase", "biomaRt"] 6431 }, 6432 "VennDetail": { 6433 "name": "VennDetail", 6434 "version": "1.26.0", 6435 "sha256": "00c07hvqk5nmmklkaxqig5zn9j0g2fp1xbisfrjmzckcyjcdmmly", 6436 "depends": ["DT", "dplyr", "ggplot2", "htmlwidgets", "magrittr", "patchwork", "plotly", "purrr", "rlang", "shiny", "tibble", "tidyr"] 6437 }, 6438 "ViSEAGO": { 6439 "name": "ViSEAGO", 6440 "version": "1.24.0", 6441 "sha256": "1mf5nmyp3n4xl555v0h8iypc3640pnc730v39n8wzmnjcq1rm9yz", 6442 "depends": ["AnnotationDbi", "AnnotationForge", "ComplexHeatmap", "DT", "DiagrammeR", "GOSemSim", "GO_db", "RColorBrewer", "R_utils", "UpSetR", "biomaRt", "circlize", "data_table", "dendextend", "dynamicTreeCut", "fgsea", "ggplot2", "heatmaply", "htmlwidgets", "igraph", "plotly", "scales", "topGO"] 6443 }, 6444 "VisiumIO": { 6445 "name": "VisiumIO", 6446 "version": "1.6.0", 6447 "sha256": "1fax22m1nvscsdq4jli6ayp3f971ymfp20kf69vka1ap1amswhli", 6448 "depends": ["BiocBaseUtils", "BiocGenerics", "BiocIO", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "TENxIO", "jsonlite"] 6449 }, 6450 "Voyager": { 6451 "name": "Voyager", 6452 "version": "1.12.0", 6453 "sha256": "1iizz27aa18banbrnv45d1pd9avwal6hwwnv4g1sqjbgz6a69sg5", 6454 "depends": ["BiocParallel", "DelayedArray", "Matrix", "MatrixGenerics", "RSpectra", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SpatialFeatureExperiment", "SummarizedExperiment", "bluster", "ggnewscale", "ggplot2", "lifecycle", "memuse", "patchwork", "rlang", "scales", "scico", "sf", "spdep", "terra", "zeallot"] 6455 }, 6456 "VplotR": { 6457 "name": "VplotR", 6458 "version": "1.20.0", 6459 "sha256": "1ljkd5yzi6yxcy0xcaqhv152vz9qfyg36ks9h24w93gynfjjl6rc", 6460 "depends": ["GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "cowplot", "ggplot2", "magrittr", "reshape2", "zoo"] 6461 }, 6462 "Wrench": { 6463 "name": "Wrench", 6464 "version": "1.28.0", 6465 "sha256": "1llv40v5hcszxxzgg1vlxgg6k8qd0g5wln4cnfj13wzayskgx9na", 6466 "depends": ["limma", "locfit", "matrixStats"] 6467 }, 6468 "XAItest": { 6469 "name": "XAItest", 6470 "version": "1.2.0", 6471 "sha256": "0yxnlxrvlz6flds58af5wg3s77jbdgcjg6bdmwl7sb6pz8pbijfg", 6472 "depends": ["DT", "SummarizedExperiment", "caret", "ggplot2", "kernelshap", "lime", "limma", "randomForest"] 6473 }, 6474 "XDE": { 6475 "name": "XDE", 6476 "version": "2.56.0", 6477 "sha256": "144ab9pav8bm3fwk8ywlsra1c0n7i33f2461a0zj54ygv1b9hf5m", 6478 "depends": ["Biobase", "BiocGenerics", "GeneMeta", "RColorBrewer", "genefilter", "gtools", "mvtnorm", "siggenes"] 6479 }, 6480 "XINA": { 6481 "name": "XINA", 6482 "version": "1.28.0", 6483 "sha256": "1kr6hybs8p86x7l5wxa35kvwq7rmsjl60blfs9xi9c8sqrrgh6dh", 6484 "depends": ["STRINGdb", "alluvial", "ggplot2", "gridExtra", "igraph", "mclust", "plyr"] 6485 }, 6486 "XVector": { 6487 "name": "XVector", 6488 "version": "0.50.0", 6489 "sha256": "1473icy90p04ai0swk0ja681x3x00a740n0i81y3ih65si5x0qy9", 6490 "depends": ["BiocGenerics", "IRanges", "S4Vectors"] 6491 }, 6492 "XeniumIO": { 6493 "name": "XeniumIO", 6494 "version": "1.2.0", 6495 "sha256": "1m5dy80g2jwws8w9y1zk3x4mlxk2zcplyy6lm27k09na83a5iq9j", 6496 "depends": ["BiocBaseUtils", "BiocGenerics", "BiocIO", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "TENxIO", "VisiumIO", "jsonlite"] 6497 }, 6498 "Xeva": { 6499 "name": "Xeva", 6500 "version": "1.26.0", 6501 "sha256": "14icm4q5kk95af721c27kgcza30ws28sinj5l76v2z60if9052k0", 6502 "depends": ["BBmisc", "Biobase", "ComplexHeatmap", "PharmacoGx", "Rmisc", "doParallel", "downloader", "ggplot2", "nlme", "scales"] 6503 }, 6504 "YAPSA": { 6505 "name": "YAPSA", 6506 "version": "1.36.0", 6507 "sha256": "0i6s8vhk8ar62g9fzn5zr76w94i11qy7g7gfbbk3kmvg3g4rrj4c", 6508 "depends": ["BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "ComplexHeatmap", "GenomicRanges", "GetoptLong", "KEGGREST", "PMCMRplus", "Seqinfo", "SomaticSignatures", "VariantAnnotation", "circlize", "corrplot", "dendextend", "doParallel", "dplyr", "ggbeeswarm", "ggplot2", "gridExtra", "gtrellis", "limSolve", "magrittr", "pracma", "reshape2"] 6509 }, 6510 "ZygosityPredictor": { 6511 "name": "ZygosityPredictor", 6512 "version": "1.10.0", 6513 "sha256": "00nckxl38ajbzxlm011x3zx2q3ka844q6f4fxhyvd8587dl1qlxd", 6514 "depends": ["DelayedArray", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "VariantAnnotation", "dplyr", "igraph", "knitr", "magrittr", "purrr", "readr", "rlang", "stringr", "tibble"] 6515 }, 6516 "a4": { 6517 "name": "a4", 6518 "version": "1.58.0", 6519 "sha256": "0smiq7apng2jlqn0l38q2h69a42zl7mqnyx94fy2m7mmdhhkdq0d", 6520 "depends": ["a4Base", "a4Classif", "a4Core", "a4Preproc", "a4Reporting"] 6521 }, 6522 "a4Base": { 6523 "name": "a4Base", 6524 "version": "1.58.0", 6525 "sha256": "1xmgg601w9lscc25ryny42qrvvsj511whxgg1fzfqzzmlrmrx267", 6526 "depends": ["Biobase", "a4Core", "a4Preproc", "annaffy", "genefilter", "glmnet", "gplots", "limma", "mpm", "multtest"] 6527 }, 6528 "a4Classif": { 6529 "name": "a4Classif", 6530 "version": "1.58.0", 6531 "sha256": "1kfj5pk7canxb4i70sk808ibinfy96418s9ni7r31gi3h1240516", 6532 "depends": ["Biobase", "ROCR", "a4Core", "a4Preproc", "glmnet", "pamr", "varSelRF"] 6533 }, 6534 "a4Core": { 6535 "name": "a4Core", 6536 "version": "1.58.0", 6537 "sha256": "10lg59fqsa4vv0sv1nrsaxmirwh6likr14b5cai5p45gya3fgbz4", 6538 "depends": ["Biobase", "glmnet"] 6539 }, 6540 "a4Preproc": { 6541 "name": "a4Preproc", 6542 "version": "1.58.0", 6543 "sha256": "0fl9vlndbj8skhn0kl1zpy10g5fjzi36h5pyf8706c6gbfxhkifg", 6544 "depends": ["Biobase", "BiocGenerics"] 6545 }, 6546 "a4Reporting": { 6547 "name": "a4Reporting", 6548 "version": "1.58.0", 6549 "sha256": "1q5s52swbkvzz3qghr03m7m17s7qvc8aaymxxaingkwavgsln77c", 6550 "depends": ["xtable"] 6551 }, 6552 "aCGH": { 6553 "name": "aCGH", 6554 "version": "1.88.0", 6555 "sha256": "1hqx009xq4j55qdxy3gwgsji0rnj069yj20xfb390ciwa2b1hixk", 6556 "depends": ["Biobase", "cluster", "multtest", "survival"] 6557 }, 6558 "abseqR": { 6559 "name": "abseqR", 6560 "version": "1.28.0", 6561 "sha256": "0cgphb2dgh6kdrr8v5zzrdrigvqribwasjhpdnfyldaxvn97b93n", 6562 "depends": ["BiocParallel", "BiocStyle", "RColorBrewer", "VennDiagram", "circlize", "flexdashboard", "ggcorrplot", "ggdendro", "ggplot2", "gridExtra", "knitr", "plotly", "plyr", "png", "reshape2", "rmarkdown", "stringr", "vegan"] 6563 }, 6564 "acde": { 6565 "name": "acde", 6566 "version": "1.40.0", 6567 "sha256": "12h52jsc7ql3hj47f1akqpcq5sh3yjrgp5zyz6d4bbsgddy30d4d", 6568 "depends": ["boot"] 6569 }, 6570 "adSplit": { 6571 "name": "adSplit", 6572 "version": "1.80.0", 6573 "sha256": "0iqyr96s8hclxvcb3ms2gsrwl2kh84ccdcg26ssvr0w15kh7gwg9", 6574 "depends": ["AnnotationDbi", "Biobase", "GO_db", "KEGGREST", "cluster", "multtest"] 6575 }, 6576 "adductomicsR": { 6577 "name": "adductomicsR", 6578 "version": "1.26.0", 6579 "sha256": "0bnhbv344qxfx96z6bjmqn5r8k12i674ip7bw364y3b63swcf7ll", 6580 "depends": ["AnnotationHub", "DT", "ExperimentHub", "OrgMassSpecR", "RcppEigen", "adductData", "ade4", "bootstrap", "data_table", "doSNOW", "dplyr", "fastcluster", "foreach", "fpc", "mzR", "pastecs", "pracma", "reshape2", "rvest", "smoother", "zoo"] 6581 }, 6582 "adverSCarial": { 6583 "name": "adverSCarial", 6584 "version": "1.8.0", 6585 "sha256": "0fpgsfmmr4skkry0r95492pm1wlvw7y8q82snzahbc3nbws0y27x", 6586 "depends": ["DelayedArray", "S4Vectors", "gtools"] 6587 }, 6588 "affxparser": { 6589 "name": "affxparser", 6590 "version": "1.82.0", 6591 "sha256": "019fq9l77s57k163b7myz50i0zs98gcqvzh1rjg4w6mqivnsp89w", 6592 "depends": [] 6593 }, 6594 "affy": { 6595 "name": "affy", 6596 "version": "1.88.0", 6597 "sha256": "0jrm1x6wygss4qg338599018izxygvzs0ddlni53pdi7j1f7aw4y", 6598 "depends": ["Biobase", "BiocGenerics", "BiocManager", "affyio", "preprocessCore"] 6599 }, 6600 "affyContam": { 6601 "name": "affyContam", 6602 "version": "1.68.0", 6603 "sha256": "1b6akkpaij3jisckh73q3k19x607afdn2ppvp2h7wn9h8h9pljwj", 6604 "depends": ["Biobase", "affy", "affydata"] 6605 }, 6606 "affyILM": { 6607 "name": "affyILM", 6608 "version": "1.62.0", 6609 "sha256": "1z0ppsd26frcshxbqwwrf5k79zhicc7cg8qfcyhqj3k696dviaxm", 6610 "depends": ["Biobase", "affxparser", "affy", "gcrma"] 6611 }, 6612 "affyPLM": { 6613 "name": "affyPLM", 6614 "version": "1.86.0", 6615 "sha256": "07hbw8q2cqh8ar7y5q6kazl46lqw0k0gg0ckmigcs4551bbsxgp6", 6616 "depends": ["Biobase", "BiocGenerics", "affy", "gcrma", "preprocessCore"] 6617 }, 6618 "affycomp": { 6619 "name": "affycomp", 6620 "version": "1.86.0", 6621 "sha256": "03h013gr7l5g7fgbs58bhqb4xblr3bfqkwqir655ck4xls1ywrb9", 6622 "depends": ["Biobase"] 6623 }, 6624 "affycoretools": { 6625 "name": "affycoretools", 6626 "version": "1.82.0", 6627 "sha256": "04vbbj8rvpxk3xpgisix6qd92383zyanxx06300ws2agh5wqwx10", 6628 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "GOstats", "Glimma", "RSQLite", "ReportingTools", "S4Vectors", "affy", "edgeR", "gcrma", "ggplot2", "gplots", "hwriter", "lattice", "limma", "oligoClasses", "xtable"] 6629 }, 6630 "affyio": { 6631 "name": "affyio", 6632 "version": "1.80.0", 6633 "sha256": "1qnxxixskak3259rs1smpc7w51ycilb510rlqas4wq53ckwbmhql", 6634 "depends": [] 6635 }, 6636 "affylmGUI": { 6637 "name": "affylmGUI", 6638 "version": "1.84.0", 6639 "sha256": "0rpfx60qsx0ia0xx1r0bhv44sh376z10dsgk903y80pfazrd3jn9", 6640 "depends": ["AnnotationDbi", "BiocGenerics", "BiocManager", "R2HTML", "affy", "affyPLM", "affyio", "gcrma", "limma", "tkrplot", "xtable"] 6641 }, 6642 "aggregateBioVar": { 6643 "name": "aggregateBioVar", 6644 "version": "1.20.0", 6645 "sha256": "0wk6y4crv1xwapccpk5cd0klr93v94q8w0x9r0m0cpqc38a052s7", 6646 "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "rlang", "tibble"] 6647 }, 6648 "agilp": { 6649 "name": "agilp", 6650 "version": "3.42.0", 6651 "sha256": "1hw15kv5f543wjzwc0ky41l2vnjax2p8pjszx3x5iwzlvjb5xsca", 6652 "depends": [] 6653 }, 6654 "airpart": { 6655 "name": "airpart", 6656 "version": "1.18.0", 6657 "sha256": "0bgz8pnjy9vxzbl6f7cn81mcs5wwqwjzdnlfciskzmk0wnn7k8sg", 6658 "depends": ["ComplexHeatmap", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "apeglm", "clue", "dplyr", "dynamicTreeCut", "emdbook", "forestplot", "ggplot2", "lpSolve", "matrixStats", "mclust", "pbapply", "plyr", "rlang", "scater", "smurf"] 6659 }, 6660 "alabaster": { 6661 "name": "alabaster", 6662 "version": "1.10.0", 6663 "sha256": "1vn835gjadgjh3fw3h2qw9i7fdyaxgsyba3l6kfgqa9vq6l81x28", 6664 "depends": ["alabaster_base", "alabaster_bumpy", "alabaster_mae", "alabaster_matrix", "alabaster_ranges", "alabaster_sce", "alabaster_se", "alabaster_spatial", "alabaster_string", "alabaster_vcf"] 6665 }, 6666 "alabaster_base": { 6667 "name": "alabaster.base", 6668 "version": "1.10.0", 6669 "sha256": "03bjpa6r8cin45gmxsdf232c15fj2r5i5kg33h748qxzip376vmj", 6670 "depends": ["Rcpp", "Rhdf5lib", "S4Vectors", "alabaster_schemas", "assorthead", "jsonlite", "jsonvalidate", "rhdf5"] 6671 }, 6672 "alabaster_bumpy": { 6673 "name": "alabaster.bumpy", 6674 "version": "1.10.0", 6675 "sha256": "1yrall9sh84gv550rd0w9qyvr6w06dw5zhdq5a9qrjkc81vzmn4p", 6676 "depends": ["BiocGenerics", "BumpyMatrix", "IRanges", "Matrix", "S4Vectors", "alabaster_base", "rhdf5"] 6677 }, 6678 "alabaster_files": { 6679 "name": "alabaster.files", 6680 "version": "1.8.0", 6681 "sha256": "0648rlmllm46ffh807wq670p2v3pfs3y2pwmh0dpb8svqx02pmc5", 6682 "depends": ["BiocGenerics", "Rsamtools", "S4Vectors", "alabaster_base"] 6683 }, 6684 "alabaster_mae": { 6685 "name": "alabaster.mae", 6686 "version": "1.10.0", 6687 "sha256": "1fqq06gx8zxx4ika3yh880xy5y40d71yai7468azlhg24chj6342", 6688 "depends": ["MultiAssayExperiment", "S4Vectors", "alabaster_base", "alabaster_se", "jsonlite", "rhdf5"] 6689 }, 6690 "alabaster_matrix": { 6691 "name": "alabaster.matrix", 6692 "version": "1.10.0", 6693 "sha256": "117ai8v7snbs2kgw9fihp8rzqxgaq19l1jscdickq2k5ci985hdd", 6694 "depends": ["BiocGenerics", "DelayedArray", "HDF5Array", "Matrix", "Rcpp", "S4Arrays", "S4Vectors", "SparseArray", "alabaster_base", "rhdf5"] 6695 }, 6696 "alabaster_ranges": { 6697 "name": "alabaster.ranges", 6698 "version": "1.10.0", 6699 "sha256": "0vlsrp3s21fq6g3w2ryp9kcclnh7m174l3a7rxk22yanfy65jmgm", 6700 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "alabaster_base", "rhdf5"] 6701 }, 6702 "alabaster_sce": { 6703 "name": "alabaster.sce", 6704 "version": "1.10.0", 6705 "sha256": "0lgymw7g2ph24f6j95zqjmh5zwn5z8lfn17bdn0wj83hrrrkcwlb", 6706 "depends": ["SingleCellExperiment", "alabaster_base", "alabaster_se", "jsonlite"] 6707 }, 6708 "alabaster_schemas": { 6709 "name": "alabaster.schemas", 6710 "version": "1.10.0", 6711 "sha256": "1zg72g6krc1jf4izghqg3shn2zdrvsqljdbhvifismca7bqqn80a", 6712 "depends": [] 6713 }, 6714 "alabaster_se": { 6715 "name": "alabaster.se", 6716 "version": "1.10.0", 6717 "sha256": "0298m0a16ibfkjsimf35qq0dj8pvzw0y762d6mxajrhbhby8bggs", 6718 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "alabaster_base", "alabaster_matrix", "alabaster_ranges", "jsonlite"] 6719 }, 6720 "alabaster_sfe": { 6721 "name": "alabaster.sfe", 6722 "version": "1.2.0", 6723 "sha256": "1306n9l8xr29pgh77yqsdi5ns3vm80d6i22pyzlxjb0c6j16h9xa", 6724 "depends": ["EBImage", "RBioFormats", "S4Vectors", "SingleCellExperiment", "SpatialFeatureExperiment", "SummarizedExperiment", "alabaster_base", "alabaster_sce", "alabaster_spatial", "jsonlite", "sfarrow", "spatialreg", "spdep", "terra", "xml2"] 6725 }, 6726 "alabaster_spatial": { 6727 "name": "alabaster.spatial", 6728 "version": "1.10.0", 6729 "sha256": "022zqn8kvnxm2zlra2w9i43g8lvbiqhjwajkyzkj3pd98i59j41v", 6730 "depends": ["S4Vectors", "SpatialExperiment", "alabaster_base", "alabaster_sce", "rhdf5"] 6731 }, 6732 "alabaster_string": { 6733 "name": "alabaster.string", 6734 "version": "1.10.0", 6735 "sha256": "01m93r7v9b00jc8spmfash7c85niw5bhd60bj2hmvmww0wdmrsqb", 6736 "depends": ["Biostrings", "S4Vectors", "alabaster_base"] 6737 }, 6738 "alabaster_vcf": { 6739 "name": "alabaster.vcf", 6740 "version": "1.10.0", 6741 "sha256": "1r92dy7qgnz4jqmqv6dinj1g7bs5axylr9yyg41d5h9mcax6vnpn", 6742 "depends": ["Rsamtools", "S4Vectors", "VariantAnnotation", "alabaster_base", "alabaster_se", "alabaster_string"] 6743 }, 6744 "alevinQC": { 6745 "name": "alevinQC", 6746 "version": "1.26.0", 6747 "sha256": "0nr21wsfh3an9bczl26xlhmwh2kq21qyjmk5a940w83l1pj6l4q8", 6748 "depends": ["DT", "GGally", "Rcpp", "cowplot", "dplyr", "ggplot2", "rjson", "rlang", "rmarkdown", "shiny", "shinydashboard", "tximport"] 6749 }, 6750 "altcdfenvs": { 6751 "name": "altcdfenvs", 6752 "version": "2.72.0", 6753 "sha256": "0b0cak4dk33h1nqi81xyz7b7hdmkd30zg2lnbrm9bdml0sm5c15c", 6754 "depends": ["Biobase", "BiocGenerics", "Biostrings", "S4Vectors", "affy", "hypergraph", "makecdfenv"] 6755 }, 6756 "anansi": { 6757 "name": "anansi", 6758 "version": "1.0.0", 6759 "sha256": "0vhj83nv9lnzppijvinm9xargcgsbhpy8475krxp79byb1qpqb52", 6760 "depends": ["Matrix", "MultiAssayExperiment", "S4Vectors", "S7", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "forcats", "ggforce", "ggplot2", "ggraph", "igraph", "patchwork", "rlang", "tidygraph"] 6761 }, 6762 "anglemania": { 6763 "name": "anglemania", 6764 "version": "1.0.0", 6765 "sha256": "0qbhixgn96iq1f10kyfggq5kvvsx03agd547w8pl48pavrs3qrmv", 6766 "depends": ["Matrix", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bigparallelr", "bigstatsr", "checkmate", "digest", "dplyr", "pbapply", "rmio", "tidyr", "withr"] 6767 }, 6768 "animalcules": { 6769 "name": "animalcules", 6770 "version": "1.26.0", 6771 "sha256": "1a614al4vh6fzmzw8v8r1hn0fpmazrqfzspvmwg8injg36ab1i9x", 6772 "depends": ["DESeq2", "DT", "GUniFrac", "Matrix", "MultiAssayExperiment", "ROCit", "S4Vectors", "SummarizedExperiment", "XML", "ape", "assertthat", "caret", "covr", "dplyr", "forcats", "ggforce", "ggplot2", "lattice", "limma", "magrittr", "plotly", "rentrez", "reshape2", "scales", "shiny", "shinyjs", "tibble", "tidyr", "tsne", "umap", "vegan"] 6773 }, 6774 "annaffy": { 6775 "name": "annaffy", 6776 "version": "1.82.0", 6777 "sha256": "0rn29k1ywsnblqn8zkfqg4x719ghz7i6h6k730yypba38h929h51", 6778 "depends": ["AnnotationDbi", "Biobase", "BiocManager", "DBI", "GO_db"] 6779 }, 6780 "anndataR": { 6781 "name": "anndataR", 6782 "version": "1.0.0", 6783 "sha256": "1lyf491kqjg07n1p9w9nraz3piz9shd119y2b8p0sifqkvp8pvzy", 6784 "depends": ["Matrix", "R6", "cli", "lifecycle", "purrr", "reticulate", "rlang"] 6785 }, 6786 "annmap": { 6787 "name": "annmap", 6788 "version": "1.52.0", 6789 "sha256": "0s5shla97scq17zc336l4mjmshrj63jcawcy3c06p8msbjgay5y8", 6790 "depends": ["Biobase", "BiocGenerics", "DBI", "GenomicRanges", "IRanges", "RMySQL", "Rsamtools", "digest", "genefilter", "lattice"] 6791 }, 6792 "annotate": { 6793 "name": "annotate", 6794 "version": "1.88.0", 6795 "sha256": "1ry6111qca2cx2fav5rk6sdwcng64lv2ahjhggixzflmag4gjqnq", 6796 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "XML", "httr", "xtable"] 6797 }, 6798 "annotationTools": { 6799 "name": "annotationTools", 6800 "version": "1.84.0", 6801 "sha256": "18rn954nrv2dil6hhkmjh3zyihyn8zc5nqdrp63i6ya66602q7g8", 6802 "depends": ["Biobase"] 6803 }, 6804 "annotatr": { 6805 "name": "annotatr", 6806 "version": "1.36.0", 6807 "sha256": "02l3xq8mgpabd9j57r40aqv8yd63yarrv2hlbapf3cr516n2hcks", 6808 "depends": ["AnnotationDbi", "AnnotationHub", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "dplyr", "ggplot2", "readr", "regioneR", "reshape2", "rlang", "rtracklayer"] 6809 }, 6810 "anota": { 6811 "name": "anota", 6812 "version": "1.58.0", 6813 "sha256": "15lyasxjsf812gx3ylhl4ajsvbpl8l685wp18gln97qq77l9ldcr", 6814 "depends": ["multtest", "qvalue"] 6815 }, 6816 "anota2seq": { 6817 "name": "anota2seq", 6818 "version": "1.32.0", 6819 "sha256": "0kx8jfidm763rw3zhyr18995k3hrgn701k71awwymghagymm2w8n", 6820 "depends": ["DESeq2", "RColorBrewer", "SummarizedExperiment", "edgeR", "limma", "multtest", "qvalue"] 6821 }, 6822 "antiProfiles": { 6823 "name": "antiProfiles", 6824 "version": "1.50.0", 6825 "sha256": "0hj48iq6cz231yasqnb564aqpp9k69v9hqh49shj39s81cral2wp", 6826 "depends": ["locfit", "matrixStats"] 6827 }, 6828 "apComplex": { 6829 "name": "apComplex", 6830 "version": "2.76.0", 6831 "sha256": "0x2ylr3fv0p88ydnibnzdaz4388vl9af893cc0rq1brrcccsdwhl", 6832 "depends": ["RBGL", "Rgraphviz", "graph", "org_Sc_sgd_db"] 6833 }, 6834 "apeglm": { 6835 "name": "apeglm", 6836 "version": "1.32.0", 6837 "sha256": "1my4y7pgl162xv643fj5klsy100mdyyxa7g1l8dwwy134n3ydqch", 6838 "depends": ["GenomicRanges", "Rcpp", "RcppEigen", "RcppNumerical", "SummarizedExperiment", "emdbook"] 6839 }, 6840 "appreci8R": { 6841 "name": "appreci8R", 6842 "version": "1.28.0", 6843 "sha256": "0wkscw6hqqzpis0mf1ixlsaf2z52imriyl5mdb5kmnxgrbv172x9", 6844 "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "COSMIC_67", "DT", "GenomicFeatures", "GenomicRanges", "GenomicScores", "Homo_sapiens", "IRanges", "MafDb_1Kgenomes_phase3_hs37d5", "MafDb_ExAC_r1_0_hs37d5", "MafDb_gnomADex_r2_1_hs37d5", "PolyPhen_Hsapiens_dbSNP131", "Rsamtools", "S4Vectors", "SIFT_Hsapiens_dbSNP137", "SNPlocs_Hsapiens_dbSNP144_GRCh37", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "VariantAnnotation", "XtraSNPlocs_Hsapiens_dbSNP144_GRCh37", "openxlsx", "rentrez", "seqinr", "shiny", "shinyjs", "stringr"] 6845 }, 6846 "aroma_light": { 6847 "name": "aroma.light", 6848 "version": "3.40.0", 6849 "sha256": "1jr8x2hiby46a3n456nnpsjdq37b0f429jh8mlia4zg1wy64bws8", 6850 "depends": ["R_methodsS3", "R_oo", "R_utils", "matrixStats"] 6851 }, 6852 "arrayMvout": { 6853 "name": "arrayMvout", 6854 "version": "1.68.0", 6855 "sha256": "0fwss499m64ilf2adk3l71w3xgqbj3lr2g72xwq95a4nz8vvlic2", 6856 "depends": ["Biobase", "affy", "affyContam", "lumi", "mdqc", "parody"] 6857 }, 6858 "arrayQuality": { 6859 "name": "arrayQuality", 6860 "version": "1.88.0", 6861 "sha256": "1nkq6ys02jjinprbphikm9pym17bvvh7d5wrpl0jyj7x9jabw443", 6862 "depends": ["RColorBrewer", "gridBase", "hexbin", "limma", "marray"] 6863 }, 6864 "artMS": { 6865 "name": "artMS", 6866 "version": "1.28.0", 6867 "sha256": "0sdxcaklcfqjad5kz5lskv04x2p8wxspav7avaznx6wz2xsx68wh", 6868 "depends": ["AnnotationDbi", "MSstats", "RColorBrewer", "UpSetR", "VennDiagram", "bit64", "circlize", "cluster", "corrplot", "data_table", "dplyr", "getopt", "ggdendro", "ggplot2", "ggrepel", "gplots", "limma", "openxlsx", "org_Hs_eg_db", "pheatmap", "plotly", "plyr", "scales", "seqinr", "stringr", "tidyr", "yaml"] 6869 }, 6870 "assorthead": { 6871 "name": "assorthead", 6872 "version": "1.4.0", 6873 "sha256": "0ysi3ak87pg7b5iqj9dnwkx11xdrqs0lfcw4q835lrswg92sf9gx", 6874 "depends": [] 6875 }, 6876 "atSNP": { 6877 "name": "atSNP", 6878 "version": "1.26.0", 6879 "sha256": "12jkk8pabndcavb284ncgxxxlw43bfgcpa5nkp6wchzfyqjzcind", 6880 "depends": ["BSgenome", "BiocFileCache", "BiocParallel", "Rcpp", "data_table", "ggplot2", "lifecycle", "motifStack", "rappdirs", "testthat"] 6881 }, 6882 "atena": { 6883 "name": "atena", 6884 "version": "1.16.0", 6885 "sha256": "02jbsk6inh63pcsandwik8cc0dd1q30raddkgxs7pszwlkdk1q73", 6886 "depends": ["AnnotationHub", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "Rsamtools", "S4Vectors", "SQUAREM", "Seqinfo", "SummarizedExperiment", "cli", "matrixStats", "sparseMatrixStats"] 6887 }, 6888 "attract": { 6889 "name": "attract", 6890 "version": "1.62.0", 6891 "sha256": "14ni9c36gar0cny7dyp433a9fmh96z9l553jwfpvl3hw02g038f7", 6892 "depends": ["AnnotationDbi", "Biobase", "GOstats", "KEGGREST", "cluster", "limma", "org_Hs_eg_db", "reactome_db"] 6893 }, 6894 "autonomics": { 6895 "name": "autonomics", 6896 "version": "1.18.0", 6897 "sha256": "02ygvvvkypwdi5rq9xjym4l4wzxn4v6h73nl426cx20q6x7wm33s", 6898 "depends": ["BiocFileCache", "BiocGenerics", "MultiAssayExperiment", "RColorBrewer", "R_utils", "S4Vectors", "SummarizedExperiment", "abind", "arrow", "bit64", "cluster", "codingMatrices", "colorspace", "data_table", "dplyr", "edgeR", "ggforce", "ggplot2", "ggrepel", "gridExtra", "limma", "lme4", "magrittr", "matrixStats", "readxl", "rlang", "scales", "stringi", "survival", "tidyr", "tidyselect", "vsn"] 6899 }, 6900 "awst": { 6901 "name": "awst", 6902 "version": "1.18.0", 6903 "sha256": "0caffj4k54qsc2py2411442n7m7bwchxk9lnc8cpbx2v18g546k9", 6904 "depends": ["SummarizedExperiment"] 6905 }, 6906 "bacon": { 6907 "name": "bacon", 6908 "version": "1.38.0", 6909 "sha256": "09y0q0dqpay4ag3wmwhqjk140cc44l3a6k3f4fiv47b3cmq50qpg", 6910 "depends": ["BiocParallel", "ellipse", "ggplot2"] 6911 }, 6912 "ballgown": { 6913 "name": "ballgown", 6914 "version": "2.42.0", 6915 "sha256": "1c7vy10ga3cswsqwxljbgqlsjg0d2lx9srfknbjy4fkbyrjci15k", 6916 "depends": ["Biobase", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "Seqinfo", "limma", "rtracklayer", "sva"] 6917 }, 6918 "bambu": { 6919 "name": "bambu", 6920 "version": "3.12.0", 6921 "sha256": "0bdwild1lxnizkwlcscl9vjnhqiri79p8vwkgw5a2lxkfj1gz1p8", 6922 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rcpp", "RcppArmadillo", "Rsamtools", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "tidyr", "xgboost"] 6923 }, 6924 "bamsignals": { 6925 "name": "bamsignals", 6926 "version": "1.42.0", 6927 "sha256": "03lqryry0jyangihscjmbsvy3s2skz50jwnl25vb44wzqkqxgmvl", 6928 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "Rcpp", "Rhtslib"] 6929 }, 6930 "bandle": { 6931 "name": "bandle", 6932 "version": "1.14.0", 6933 "sha256": "1nydm87m1knayzs6sz208z2bxr6caabb60p37268cix9x1941qp4", 6934 "depends": ["BH", "Biobase", "BiocParallel", "BiocStyle", "MSnbase", "RColorBrewer", "Rcpp", "RcppArmadillo", "S4Vectors", "circlize", "coda", "dplyr", "ggalluvial", "ggplot2", "ggrepel", "gridExtra", "gtools", "knitr", "lbfgs", "pRoloc", "pRolocdata", "plyr", "rlang", "robustbase", "tidyr"] 6935 }, 6936 "banocc": { 6937 "name": "banocc", 6938 "version": "1.34.0", 6939 "sha256": "0y2capm8b2dx68myybzgf74khm22rjqihg9l1g03xpv1k19jlc90", 6940 "depends": ["coda", "mvtnorm", "rstan", "stringr"] 6941 }, 6942 "barbieQ": { 6943 "name": "barbieQ", 6944 "version": "1.2.0", 6945 "sha256": "19zzrw4y0lar36pz8izniy5rdck7jn5wy7aqlp6qwrqwim9yl52m", 6946 "depends": ["ComplexHeatmap", "S4Vectors", "SummarizedExperiment", "circlize", "data_table", "dplyr", "ggplot2", "igraph", "limma", "logistf", "magrittr", "tidyr"] 6947 }, 6948 "basecallQC": { 6949 "name": "basecallQC", 6950 "version": "1.34.0", 6951 "sha256": "1yyz87r8wcwsggfbrbpy8xiqqs7i4zqw1mqjd0hfyx6yja4kp7fz", 6952 "depends": ["DT", "ShortRead", "XML", "data_table", "dplyr", "ggplot2", "knitr", "lazyeval", "magrittr", "prettydoc", "raster", "rmarkdown", "stringr", "tidyr", "yaml"] 6953 }, 6954 "basilisk": { 6955 "name": "basilisk", 6956 "version": "1.22.0", 6957 "sha256": "0127ilysjfp7d2nhrrxd84jk9r6flcgk5f1wgy7r9ivyw484023a", 6958 "depends": ["dir_expiry", "reticulate"] 6959 }, 6960 "basilisk_utils": { 6961 "name": "basilisk.utils", 6962 "version": "1.22.0", 6963 "sha256": "1pqdkfg7jifl52ada9d70xhbhknm54g9wzxsnca0q9plgpiddmz9", 6964 "depends": ["dir_expiry"] 6965 }, 6966 "batchCorr": { 6967 "name": "batchCorr", 6968 "version": "1.0.0", 6969 "sha256": "08n9k14fwhljp2mfcyza0zwsd04kwnk1w4x76mgi8bn9r6a60vgr", 6970 "depends": ["BiocParallel", "SummarizedExperiment", "mclust", "reshape"] 6971 }, 6972 "batchelor": { 6973 "name": "batchelor", 6974 "version": "1.26.0", 6975 "sha256": "0s991n072s7vbcj2ad5zh079iwwcqx92m6h0wmif3wma0qpw16g2", 6976 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "Matrix", "Rcpp", "ResidualMatrix", "S4Vectors", "ScaledMatrix", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat", "igraph", "scuttle"] 6977 }, 6978 "bayNorm": { 6979 "name": "bayNorm", 6980 "version": "1.28.0", 6981 "sha256": "0cpc1l8xsmzz8qfc9izq6a6ajv8bl3yrv64qhji3nq9bv4ln5f7z", 6982 "depends": ["BB", "BiocParallel", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "RcppProgress", "SingleCellExperiment", "SummarizedExperiment", "doSNOW", "fitdistrplus", "foreach", "iterators", "locfit"] 6983 }, 6984 "baySeq": { 6985 "name": "baySeq", 6986 "version": "2.44.0", 6987 "sha256": "0zljz45xcixipyprirvvzyx9v2hjbwr6wdv9zz0b8gpdriv5c0g0", 6988 "depends": ["GenomicRanges", "abind", "edgeR"] 6989 }, 6990 "bcSeq": { 6991 "name": "bcSeq", 6992 "version": "1.32.0", 6993 "sha256": "0r2qdn676lfmk56id0v6ahj2v6ajaxgsrgr2x8slzw6zijybvlsc", 6994 "depends": ["Biostrings", "Matrix", "Rcpp"] 6995 }, 6996 "beachmat": { 6997 "name": "beachmat", 6998 "version": "2.26.0", 6999 "sha256": "1s2v4d49yc1r1cla1p54zkcw14bazgz8fmzb1khqngbi26apmk0p", 7000 "depends": ["BiocGenerics", "DelayedArray", "Matrix", "Rcpp", "SparseArray", "assorthead"] 7001 }, 7002 "beachmat_hdf5": { 7003 "name": "beachmat.hdf5", 7004 "version": "1.8.0", 7005 "sha256": "0dp8p111ar64syvh4x7s4rwjj4vhil1c09r5am48c0cg789qx49y", 7006 "depends": ["DelayedArray", "HDF5Array", "Rcpp", "Rhdf5lib", "assorthead", "beachmat"] 7007 }, 7008 "beachmat_tiledb": { 7009 "name": "beachmat.tiledb", 7010 "version": "1.2.0", 7011 "sha256": "1x6nz89mjp83qh70c3bbrq8zfb6fk0pv75hsnhi7dsvk1sp9d537", 7012 "depends": ["DelayedArray", "Rcpp", "TileDBArray", "assorthead", "beachmat", "tiledb"] 7013 }, 7014 "bedbaser": { 7015 "name": "bedbaser", 7016 "version": "1.2.0", 7017 "sha256": "13ncvwpm7zplyhkqg8pmn4nkd4lv2dgwb2pjr25xciji4ixgdcmq", 7018 "depends": ["AnVIL", "BiocFileCache", "GenomeInfoDb", "GenomicRanges", "R_utils", "dplyr", "httr", "purrr", "rlang", "rtracklayer", "stringr", "tibble", "tidyr"] 7019 }, 7020 "beer": { 7021 "name": "beer", 7022 "version": "1.14.0", 7023 "sha256": "0c3plk1cibcka6ky043h98ibqsy8nmhs812n3bvafq9w3wz6dch0", 7024 "depends": ["BiocParallel", "PhIPData", "SummarizedExperiment", "cli", "edgeR", "progressr", "rjags"] 7025 }, 7026 "betaHMM": { 7027 "name": "betaHMM", 7028 "version": "1.6.0", 7029 "sha256": "00j4k8z0kfr14k3ahfzqhc3sf00ll7yvwhyjhbcwr6vi8dpm7s01", 7030 "depends": ["GenomicRanges", "S4Vectors", "SummarizedExperiment", "cowplot", "doParallel", "dplyr", "foreach", "ggplot2", "pROC", "scales", "stringr", "tidyr", "tidyselect"] 7031 }, 7032 "bettr": { 7033 "name": "bettr", 7034 "version": "1.6.0", 7035 "sha256": "1ns7jazl31w2ivbbnf3f8502nszkwsskn7rkl7kjvh9l8lrakdyw", 7036 "depends": ["ComplexHeatmap", "DT", "Hmisc", "S4Vectors", "SummarizedExperiment", "bslib", "circlize", "cowplot", "dplyr", "ggplot2", "rlang", "scales", "shiny", "shinyjqui", "sortable", "tibble", "tidyr"] 7037 }, 7038 "bigmelon": { 7039 "name": "bigmelon", 7040 "version": "1.36.0", 7041 "sha256": "0m5nc9vsm1y1mgdq7fscdnfmdxs85xml863lsyc7vxknlgpdl6yq", 7042 "depends": ["Biobase", "BiocGenerics", "GEOquery", "gdsfmt", "illuminaio", "methylumi", "minfi", "wateRmelon"] 7043 }, 7044 "bioCancer": { 7045 "name": "bioCancer", 7046 "version": "1.38.0", 7047 "sha256": "08b34kcx3h6mk9f7mlvbqpasyb0wa0vp07s685biphwl7355zdpn", 7048 "depends": ["AlgDesign", "AnnotationDbi", "Biobase", "DOSE", "DT", "DiagrammeR", "GO_db", "R_methodsS3", "R_oo", "ReactomePA", "XML", "cBioPortalData", "clusterProfiler", "dplyr", "geNetClassifier", "htmlwidgets", "org_Bt_eg_db", "org_Hs_eg_db", "plyr", "r_import", "radiant_data", "reactome_db", "shiny", "shinythemes", "tibble", "tidyr", "visNetwork"] 7049 }, 7050 "bioDist": { 7051 "name": "bioDist", 7052 "version": "1.82.0", 7053 "sha256": "1gyqvh0wpq64nw26dhycn98366yg0cgvaz7k5mxa68fh7zjy8ima", 7054 "depends": ["Biobase", "KernSmooth"] 7055 }, 7056 "bioassayR": { 7057 "name": "bioassayR", 7058 "version": "1.48.0", 7059 "sha256": "1jyw6msz40k47ai919zc2y9j13g2y745wh9r4gg794zlv092l1jg", 7060 "depends": ["BiocGenerics", "ChemmineR", "DBI", "Matrix", "RSQLite", "XML", "rjson"] 7061 }, 7062 "biobroom": { 7063 "name": "biobroom", 7064 "version": "1.42.0", 7065 "sha256": "0d4c9qqwd5zm5y9xcskfjashqkdiy0ri3gsj1kmfb5zmv8i8666s", 7066 "depends": ["Biobase", "broom", "dplyr", "tidyr"] 7067 }, 7068 "biobtreeR": { 7069 "name": "biobtreeR", 7070 "version": "1.22.0", 7071 "sha256": "0kcnphyqlr28h63ih6hy6a8kmcf3cgs0dihfkmmxmybqx7af6n43", 7072 "depends": ["httpuv", "httr", "jsonlite", "stringi"] 7073 }, 7074 "biocGraph": { 7075 "name": "biocGraph", 7076 "version": "1.72.0", 7077 "sha256": "13bc5kqvfpx2kl9hs2hcna8z73rjgdyn5cm30016f7m7xpggnkna", 7078 "depends": ["BiocGenerics", "Rgraphviz", "geneplotter", "graph"] 7079 }, 7080 "biocViews": { 7081 "name": "biocViews", 7082 "version": "1.78.0", 7083 "sha256": "1dfsfj4dm9wnh4qr1sqdrwzccl3pgw58j17vr3i1bvxkrq31p1ws", 7084 "depends": ["Biobase", "BiocManager", "RBGL", "RCurl", "RUnit", "XML", "graph"] 7085 }, 7086 "biocmake": { 7087 "name": "biocmake", 7088 "version": "1.2.0", 7089 "sha256": "1f5xbdfdg0nwlv3csszjyqb3s34369fifazd7hzys15z6y4mhqnc", 7090 "depends": ["dir_expiry"] 7091 }, 7092 "biocroxytest": { 7093 "name": "biocroxytest", 7094 "version": "1.6.0", 7095 "sha256": "14k4mk4xyi1r1r1836x73br188n3wj86s2h2szkj26hhncayy3np", 7096 "depends": ["cli", "glue", "roxygen2", "stringr"] 7097 }, 7098 "biocthis": { 7099 "name": "biocthis", 7100 "version": "1.20.0", 7101 "sha256": "0svn4156jnf1ql1ln6x0c80h7z0gkxlfcn3q644ahpi18s6w0pil", 7102 "depends": ["BiocManager", "fs", "glue", "rlang", "styler", "usethis"] 7103 }, 7104 "biodb": { 7105 "name": "biodb", 7106 "version": "1.18.0", 7107 "sha256": "0462420y1pz1h09kd3bgwz9jazaqd4yzwz5815x438lfsdj5vxvv", 7108 "depends": ["R6", "RSQLite", "Rcpp", "XML", "chk", "fscache", "jsonlite", "lgr", "lifecycle", "openssl", "plyr", "progress", "rappdirs", "sched", "sqlq", "stringr", "testthat", "withr", "yaml"] 7109 }, 7110 "biodbChebi": { 7111 "name": "biodbChebi", 7112 "version": "1.16.0", 7113 "sha256": "1kk9i3jhg982s39nvxqhpi8q7lxhdyb0scvx34fxaaqgfjb3lxkk", 7114 "depends": ["R6", "biodb"] 7115 }, 7116 "biomaRt": { 7117 "name": "biomaRt", 7118 "version": "2.66.0", 7119 "sha256": "0xvwn4s7lxd2g98x6bng4w2vvxp26s57wzq2pij4f117xscad42f", 7120 "depends": ["AnnotationDbi", "BiocFileCache", "curl", "httr2", "progress", "stringr", "xml2"] 7121 }, 7122 "biomformat": { 7123 "name": "biomformat", 7124 "version": "1.38.0", 7125 "sha256": "1ydcgifdrgg48y7qxg0gw30h332y3yk3k3n17fajkv58mlvyx1yc", 7126 "depends": ["Matrix", "jsonlite", "plyr", "rhdf5"] 7127 }, 7128 "biomvRCNS": { 7129 "name": "biomvRCNS", 7130 "version": "1.50.0", 7131 "sha256": "1avg6nzw15fs2c02yr33ny4gmnx4ygn5f3l2dk0cfxd6q6cjpjyy", 7132 "depends": ["GenomicRanges", "Gviz", "IRanges", "mvtnorm"] 7133 }, 7134 "biosigner": { 7135 "name": "biosigner", 7136 "version": "1.38.0", 7137 "sha256": "1c3sv00g1b8v8pb98riszpdwazx2wpvb2sm5vh89b7sdy4hbppfk", 7138 "depends": ["Biobase", "MultiAssayExperiment", "MultiDataSet", "SummarizedExperiment", "e1071", "randomForest", "ropls"] 7139 }, 7140 "biotmle": { 7141 "name": "biotmle", 7142 "version": "1.34.0", 7143 "sha256": "17mjhybxffr36awc85qfsdbndzin90x4xq2isi2cdag52vr6jczr", 7144 "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SummarizedExperiment", "assertthat", "dplyr", "drtmle", "ggplot2", "ggsci", "limma", "superheat", "tibble"] 7145 }, 7146 "biovizBase": { 7147 "name": "biovizBase", 7148 "version": "1.58.0", 7149 "sha256": "1fx6plg3jdy9frs7p6bmxnbkyxa06bw9iyyqlw96ifi5zarkf8vl", 7150 "depends": ["AnnotationDbi", "AnnotationFilter", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Hmisc", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "dichromat", "ensembldb", "rlang", "scales"] 7151 }, 7152 "biscuiteer": { 7153 "name": "biscuiteer", 7154 "version": "1.24.0", 7155 "sha256": "074gqvjcl8y30a6s0ivjrdf1lcyafj6l5krdd88q0ldlsik1z7fk", 7156 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "DelayedMatrixStats", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "Homo_sapiens", "IRanges", "Matrix", "Mus_musculus", "QDNAseq", "R_utils", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "biscuiteerData", "bsseq", "data_table", "dmrseq", "gtools", "impute", "matrixStats", "qualV", "readr", "rtracklayer"] 7157 }, 7158 "blacksheepr": { 7159 "name": "blacksheepr", 7160 "version": "1.24.0", 7161 "sha256": "0bb9l54wppqz8llq71riqk29mg4dibnyx62k5pk30rrzahp71m02", 7162 "depends": ["ComplexHeatmap", "RColorBrewer", "SummarizedExperiment", "circlize", "pasilla", "viridis"] 7163 }, 7164 "blase": { 7165 "name": "blase", 7166 "version": "1.0.0", 7167 "sha256": "0hg3bc0lnc47ssj2dslddq6wzkq2snjck97zbk9n4rpim0hmrwz0", 7168 "depends": ["BiocParallel", "Matrix", "MatrixGenerics", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "boot", "dplyr", "ggplot2", "mgcv", "patchwork", "rlang", "scater", "viridis"] 7169 }, 7170 "bluster": { 7171 "name": "bluster", 7172 "version": "1.20.0", 7173 "sha256": "0ghzvj8s4hy88w4rgx817zn0ipxga31q6gj713pvjlfj6bgqvjs4", 7174 "depends": ["BiocNeighbors", "BiocParallel", "Matrix", "Rcpp", "S4Vectors", "assorthead", "cluster", "igraph"] 7175 }, 7176 "bnbc": { 7177 "name": "bnbc", 7178 "version": "1.32.0", 7179 "sha256": "1p79j6a499ly3i2wil1fh6ipi2sbfhihrnajq3br0idgjyizqjsw", 7180 "depends": ["BiocGenerics", "EBImage", "GenomicRanges", "HiCBricks", "IRanges", "Rcpp", "S4Vectors", "Seqinfo", "SummarizedExperiment", "data_table", "matrixStats", "preprocessCore", "rhdf5", "sva"] 7181 }, 7182 "bnem": { 7183 "name": "bnem", 7184 "version": "1.18.0", 7185 "sha256": "1hcd98zrvgcj19k546j0kjbivjsndc4bryrj9aczkw7f7mbgzpjz", 7186 "depends": ["Biobase", "CellNOptR", "RColorBrewer", "Rgraphviz", "affy", "binom", "cluster", "epiNEM", "flexclust", "graph", "limma", "matrixStats", "mnem", "rmarkdown", "snowfall", "sva", "vsn"] 7187 }, 7188 "borealis": { 7189 "name": "borealis", 7190 "version": "1.14.0", 7191 "sha256": "018srka1f5c4yv644fq66bgj19x1mmyq97xpgg2bzp0j787721lw", 7192 "depends": ["Biobase", "DSS", "GenomicRanges", "R_utils", "bsseq", "cowplot", "doParallel", "dplyr", "foreach", "gamlss", "gamlss_dist", "ggplot2", "plyr", "purrr", "rlang", "snow"] 7193 }, 7194 "breakpointR": { 7195 "name": "breakpointR", 7196 "version": "1.28.0", 7197 "sha256": "0wmrbm1qssv9njxs3m40kag1v0xf1zrskb38vlzb2q3669gpjr9q", 7198 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "breakpointRdata", "cowplot", "doParallel", "foreach", "ggplot2", "gtools"] 7199 }, 7200 "brendaDb": { 7201 "name": "brendaDb", 7202 "version": "1.24.0", 7203 "sha256": "0snaip1b7p3b7bjzcjxmwf6ivi2lv5ksawamkksfk5h4g4vpfpa5", 7204 "depends": ["BiocFileCache", "BiocParallel", "Rcpp", "crayon", "dplyr", "magrittr", "purrr", "rappdirs", "rlang", "stringr", "tibble", "tidyr"] 7205 }, 7206 "bsseq": { 7207 "name": "bsseq", 7208 "version": "1.46.0", 7209 "sha256": "1x2d17s0dv0wmn4lw5xmq8wjbly4llaayiz47f5l115il577l4ig", 7210 "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DelayedArray", "DelayedMatrixStats", "GenomicRanges", "HDF5Array", "IRanges", "R_utils", "Rcpp", "S4Vectors", "Seqinfo", "SummarizedExperiment", "assorthead", "beachmat", "data_table", "gtools", "limma", "locfit", "permute", "rhdf5", "scales"] 7211 }, 7212 "bugsigdbr": { 7213 "name": "bugsigdbr", 7214 "version": "1.16.0", 7215 "sha256": "13mfx8g4hd7d3rdmbfsr9a7z6zkggllaj48h6sbr6h989g86sxnp", 7216 "depends": ["BiocFileCache", "vroom"] 7217 }, 7218 "bumphunter": { 7219 "name": "bumphunter", 7220 "version": "1.52.0", 7221 "sha256": "1rkfhpfi30jas48ldy6qxj1dkkij7bfq3d4xsbwzmm0ip3hdipaj", 7222 "depends": ["AnnotationDbi", "BiocGenerics", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "doRNG", "foreach", "iterators", "limma", "locfit", "matrixStats"] 7223 }, 7224 "cBioPortalData": { 7225 "name": "cBioPortalData", 7226 "version": "2.21.5", 7227 "sha256": "0by3295xq1b6di5d50zqqv7sbn6g68sgdn2fvyxd4h88sr87ypb5", 7228 "depends": ["AnVIL", "BiocBaseUtils", "BiocFileCache", "GenomicRanges", "IRanges", "MultiAssayExperiment", "RTCGAToolbox", "RaggedExperiment", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TCGAutils", "digest", "dplyr", "httr", "readr", "tibble", "tidyr"] 7229 }, 7230 "cTRAP": { 7231 "name": "cTRAP", 7232 "version": "1.28.0", 7233 "sha256": "0arpwi2iax013d3vzjxyjk7dwq99p63356wfhcilqk0mprf2sa7p", 7234 "depends": ["AnnotationDbi", "AnnotationHub", "DT", "R_utils", "binr", "cowplot", "data_table", "dplyr", "fastmatch", "fgsea", "ggplot2", "ggrepel", "highcharter", "htmltools", "httr", "limma", "pbapply", "purrr", "qs", "readxl", "reshape2", "rhdf5", "rlang", "scales", "shiny", "shinycssloaders", "tibble"] 7235 }, 7236 "cageminer": { 7237 "name": "cageminer", 7238 "version": "1.16.0", 7239 "sha256": "02ah6mgsx0gchrjx5mfhypw5c9fww4xh4a7qpj8k1v25l200q43f", 7240 "depends": ["BioNERO", "GenomeInfoDb", "GenomicRanges", "IRanges", "ggbio", "ggplot2", "ggtext", "reshape2", "rlang"] 7241 }, 7242 "calm": { 7243 "name": "calm", 7244 "version": "1.24.0", 7245 "sha256": "1p045a9phzkskllqmgk34c9bd2gcyvndzhp2vrna1qjz4dmwk93a", 7246 "depends": ["mgcv"] 7247 }, 7248 "canceR": { 7249 "name": "canceR", 7250 "version": "1.44.0", 7251 "sha256": "0famd2k80mm58vswkvkz8bv29cp23a58m0fbb3jcilyp7d0k6v97", 7252 "depends": ["Biobase", "Formula", "GSEABase", "RUnit", "R_methodsS3", "R_oo", "cBioPortalData", "circlize", "dplyr", "geNetClassifier", "phenoTest", "plyr", "rpart", "survival", "tidyr", "tkrplot"] 7253 }, 7254 "cancerclass": { 7255 "name": "cancerclass", 7256 "version": "1.54.0", 7257 "sha256": "0mj4s2yykywmwmlr8fi94r0v1aql68xpsbqgz2yh47fpvhair2kh", 7258 "depends": ["Biobase", "binom"] 7259 }, 7260 "cardelino": { 7261 "name": "cardelino", 7262 "version": "1.12.0", 7263 "sha256": "1r1dd9wmi8amv1825j74kmqjnlhxvcdqaq1g7pf48wa3qxyrylip", 7264 "depends": ["GenomeInfoDb", "GenomicRanges", "Matrix", "S4Vectors", "VariantAnnotation", "combinat", "ggplot2", "ggtree", "matrixStats", "pheatmap", "snpStats", "vcfR"] 7265 }, 7266 "casper": { 7267 "name": "casper", 7268 "version": "2.44.0", 7269 "sha256": "0kz6h9ixs3lij8d0zvf3243zczqg3wbi75xq4la3apsb73nlail2", 7270 "depends": ["Biobase", "BiocGenerics", "EBarrays", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "VGAM", "coda", "gaga", "gtools", "limma", "mgcv", "rtracklayer", "sqldf", "survival"] 7271 }, 7272 "categoryCompare": { 7273 "name": "categoryCompare", 7274 "version": "1.54.0", 7275 "sha256": "055g2qj7yjs9hxjaig3ja9v9p8is2swgxwd1ps6my1vgyk361bcv", 7276 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "Category", "GOstats", "GSEABase", "RCy3", "annotate", "colorspace", "graph", "hwriter"] 7277 }, 7278 "cbaf": { 7279 "name": "cbaf", 7280 "version": "1.32.0", 7281 "sha256": "15dzdga77mz77bjn152cw87gn84k05ijmnnxkxab25y4mdll3p1f", 7282 "depends": ["BiocFileCache", "RColorBrewer", "cBioPortalData", "genefilter", "gplots", "openxlsx", "zip"] 7283 }, 7284 "cbpManager": { 7285 "name": "cbpManager", 7286 "version": "1.18.0", 7287 "sha256": "05qihizwrz0yaqcg34mdx135ysr7kys7hnhv6xdm60ghh2l68iqd", 7288 "depends": ["DT", "basilisk", "dplyr", "htmltools", "jsonlite", "magrittr", "markdown", "plyr", "rapportools", "reticulate", "rintrojs", "rlang", "shiny", "shinyBS", "shinycssloaders", "shinydashboard", "vroom"] 7289 }, 7290 "ccImpute": { 7291 "name": "ccImpute", 7292 "version": "1.12.0", 7293 "sha256": "09g11pbrni0ifc756h393jm0bfivnx8n72iq8rz1k1sjw009xdq0", 7294 "depends": ["BiocParallel", "Matrix", "Rcpp", "RcppEigen", "SingleCellExperiment", "SummarizedExperiment", "irlba", "sparseMatrixStats"] 7295 }, 7296 "ccfindR": { 7297 "name": "ccfindR", 7298 "version": "1.30.0", 7299 "sha256": "1rxfy8dnxg047v65d27k30gnixbhzfq0fg7fx5y5adljnj352i4b", 7300 "depends": ["Matrix", "RColorBrewer", "Rcpp", "RcppEigen", "Rdpack", "Rmpi", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ape", "gtools", "irlba"] 7301 }, 7302 "ccrepe": { 7303 "name": "ccrepe", 7304 "version": "1.46.0", 7305 "sha256": "02i4izk0p7h1v96fmhjhwd7z8m2kql3akk620qv2z904ndlg8hdl", 7306 "depends": ["infotheo"] 7307 }, 7308 "ceRNAnetsim": { 7309 "name": "ceRNAnetsim", 7310 "version": "1.22.0", 7311 "sha256": "149ykxsgfhw5xmdql6nba3damxi5m8ybbpc9a8jybqxbwhsnc3ab", 7312 "depends": ["dplyr", "furrr", "future", "ggplot2", "ggraph", "igraph", "purrr", "rlang", "tibble", "tidygraph", "tidyr"] 7313 }, 7314 "celaref": { 7315 "name": "celaref", 7316 "version": "1.28.0", 7317 "sha256": "1xlkqc5880rrryrbpl4fnh5vh171imf8jlc8lxz5aygvl3hhpgvy", 7318 "depends": ["BiocGenerics", "DelayedArray", "MAST", "Matrix", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "magrittr", "readr", "rlang", "tibble"] 7319 }, 7320 "celda": { 7321 "name": "celda", 7322 "version": "1.26.0", 7323 "sha256": "1qq52kpzq20whx9v0b6l29hkghrn5m3yilhc0gz23m2cafr0nni5", 7324 "depends": ["ComplexHeatmap", "DelayedArray", "MCMCprecision", "Matrix", "RColorBrewer", "Rcpp", "RcppEigen", "Rtsne", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "data_table", "dbscan", "dendextend", "digest", "doParallel", "enrichR", "foreach", "ggdendro", "ggplot2", "ggrepel", "gridExtra", "gtable", "matrixStats", "pROC", "plyr", "reshape2", "scales", "scater", "scran", "stringr", "uwot", "withr"] 7325 }, 7326 "cellbaseR": { 7327 "name": "cellbaseR", 7328 "version": "1.34.0", 7329 "sha256": "1d7p7waavsxgqarj9jhyjara86v6xr3ipdshhldhvk70r5lm0nan", 7330 "depends": ["BiocParallel", "R_utils", "Rsamtools", "data_table", "doParallel", "foreach", "httr", "jsonlite", "pbapply", "tidyr"] 7331 }, 7332 "cellity": { 7333 "name": "cellity", 7334 "version": "1.38.0", 7335 "sha256": "0hddivf2yf670bvs41fd12nzrs0lxqsw8fcxi5jrp7awzk3v777r", 7336 "depends": ["AnnotationDbi", "e1071", "ggplot2", "mvoutlier", "org_Hs_eg_db", "org_Mm_eg_db", "robustbase", "topGO"] 7337 }, 7338 "cellmig": { 7339 "name": "cellmig", 7340 "version": "1.0.0", 7341 "sha256": "1v617x19v3a8kyy541awpfah35v7qxkhdf9by0fhrsk7igkmgdl6", 7342 "depends": ["BH", "Rcpp", "RcppEigen", "RcppParallel", "StanHeaders", "ape", "ggforce", "ggplot2", "ggtree", "patchwork", "reshape2", "rstan", "rstantools", "scales"] 7343 }, 7344 "cellmigRation": { 7345 "name": "cellmigRation", 7346 "version": "1.18.0", 7347 "sha256": "1j0bf7l780j3z6nb49g3b8yycifp1wym8zb7iy3dfx5d7i297aaz", 7348 "depends": ["FME", "FactoMineR", "Hmisc", "SpatialTools", "doParallel", "foreach", "matrixStats", "reshape2", "sp", "tiff", "vioplot"] 7349 }, 7350 "cellscape": { 7351 "name": "cellscape", 7352 "version": "1.34.0", 7353 "sha256": "1lnyqhjw78vhimwsch94qxnam3wq77x2apgr054ir9rarh38i5lj", 7354 "depends": ["dplyr", "gtools", "htmlwidgets", "jsonlite", "reshape2", "stringr"] 7355 }, 7356 "cellxgenedp": { 7357 "name": "cellxgenedp", 7358 "version": "1.14.0", 7359 "sha256": "13pab6l4r3sc47vh8mf7f2rd4ym9cjvagics29yfxpb3zdql66h6", 7360 "depends": ["DT", "cli", "curl", "dplyr", "httr", "rjsoncons", "shiny"] 7361 }, 7362 "censcyt": { 7363 "name": "censcyt", 7364 "version": "1.18.0", 7365 "sha256": "08kmpqwq3aswpkmg0n5720b6v0xwp2x8g353mwg4hd9cywjfvhhd", 7366 "depends": ["BiocParallel", "MASS", "S4Vectors", "SummarizedExperiment", "broom_mixed", "diffcyt", "dirmult", "dplyr", "edgeR", "fitdistrplus", "lme4", "magrittr", "mice", "multcomp", "purrr", "rlang", "stringr", "survival", "tibble", "tidyr"] 7367 }, 7368 "cfDNAPro": { 7369 "name": "cfDNAPro", 7370 "version": "1.16.0", 7371 "sha256": "16387in3j9i6q059l1kh64lj3kh3wd23ia2x80dm7azdlykr616l", 7372 "depends": ["BSgenome_Hsapiens_NCBI_GRCh38", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "dplyr", "ggplot2", "magrittr", "plyranges", "quantmod", "rlang", "stringr", "tibble"] 7373 }, 7374 "cfTools": { 7375 "name": "cfTools", 7376 "version": "1.10.0", 7377 "sha256": "1d9slykcph6xkbni1msnn9vmsh7rl6xddpbmllf0bv2bbxmhh6wc", 7378 "depends": ["BH", "GenomicRanges", "R_utils", "Rcpp", "basilisk", "cfToolsData"] 7379 }, 7380 "cfdnakit": { 7381 "name": "cfdnakit", 7382 "version": "1.8.0", 7383 "sha256": "0qmqmxgvjfv35xaliyr63visqkhjny8nlqbrncpmj7w6p2b1ixi5", 7384 "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "PSCBS", "QDNAseq", "Rsamtools", "S4Vectors", "dplyr", "ggplot2", "magrittr", "rlang"] 7385 }, 7386 "cghMCR": { 7387 "name": "cghMCR", 7388 "version": "1.68.0", 7389 "sha256": "1cwpi4d904s7g0rh35fqqg4d9xg5wn3h776dh4kkf94pbrrlfprc", 7390 "depends": ["BiocGenerics", "CNTools", "DNAcopy", "limma"] 7391 }, 7392 "chevreulPlot": { 7393 "name": "chevreulPlot", 7394 "version": "1.2.0", 7395 "sha256": "0hmn44ljkj26is2dbr9f412pcawi95v3n66mq7rkzqqgq6ndryni", 7396 "depends": ["ComplexHeatmap", "EnsDb_Hsapiens_v86", "S4Vectors", "SingleCellExperiment", "chevreulProcess", "circlize", "cluster", "clustree", "dplyr", "forcats", "fs", "ggplot2", "patchwork", "plotly", "purrr", "scales", "scater", "scran", "scuttle", "stringr", "tibble", "tidyr", "tidyselect", "wiggleplotr"] 7397 }, 7398 "chevreulProcess": { 7399 "name": "chevreulProcess", 7400 "version": "1.2.0", 7401 "sha256": "14h9a96skiricsdv05gcyng8drynii18s1c3ffg7py8hzkw2wxqa", 7402 "depends": ["DBI", "EnsDb_Hsapiens_v86", "GenomicFeatures", "RSQLite", "S4Vectors", "SingleCellExperiment", "batchelor", "bluster", "circlize", "cluster", "dplyr", "ensembldb", "fs", "glue", "megadepth", "purrr", "scater", "scran", "scuttle", "stringr", "tibble", "tidyr", "tidyselect"] 7403 }, 7404 "chihaya": { 7405 "name": "chihaya", 7406 "version": "1.10.0", 7407 "sha256": "1wc4bj9vsp6h06b0rwsswzsv4zx81j17pnx77hjigbcd03j9xv7l", 7408 "depends": ["DelayedArray", "HDF5Array", "Matrix", "Rcpp", "Rhdf5lib", "rhdf5"] 7409 }, 7410 "chimeraviz": { 7411 "name": "chimeraviz", 7412 "version": "1.36.0", 7413 "sha256": "12x3q9zm25qrpm4z4vlfmp8wynbxcmdw2fp486m8ys7fmdzpl0lk", 7414 "depends": ["AnnotationDbi", "AnnotationFilter", "BiocStyle", "Biostrings", "DT", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "Gviz", "IRanges", "RCircos", "RColorBrewer", "Rgraphviz", "Rsamtools", "S4Vectors", "checkmate", "data_table", "dplyr", "ensembldb", "graph", "gtools", "magick", "org_Hs_eg_db", "org_Mm_eg_db", "plyr", "rmarkdown"] 7415 }, 7416 "chipenrich": { 7417 "name": "chipenrich", 7418 "version": "2.34.0", 7419 "sha256": "0d3jda48r8q9w8pplisfbjvilyvfkm7q7bhylqzrc6v0zahlx27l", 7420 "depends": ["AnnotationDbi", "BiocGenerics", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "Seqinfo", "chipenrich_data", "lattice", "latticeExtra", "mgcv", "org_Dm_eg_db", "org_Dr_eg_db", "org_Hs_eg_db", "org_Mm_eg_db", "org_Rn_eg_db", "plyr", "rms", "rtracklayer", "stringr"] 7421 }, 7422 "chipseq": { 7423 "name": "chipseq", 7424 "version": "1.60.0", 7425 "sha256": "15vxg462svh33460xfas5kxc96nnlkprq442gplmspsiwb0jhjf3", 7426 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "ShortRead", "lattice"] 7427 }, 7428 "chopsticks": { 7429 "name": "chopsticks", 7430 "version": "1.76.0", 7431 "sha256": "120b9c8g5mm2fxf97xcmgp75x8qmnw01ih53ny6a4940wgji07as", 7432 "depends": ["survival"] 7433 }, 7434 "chromDraw": { 7435 "name": "chromDraw", 7436 "version": "2.40.0", 7437 "sha256": "09rpbaz2jds6c3h3mm50cjcdr8za8x5127pvr6mf7ly6g7qyqinp", 7438 "depends": ["GenomicRanges", "Rcpp"] 7439 }, 7440 "chromPlot": { 7441 "name": "chromPlot", 7442 "version": "1.38.0", 7443 "sha256": "0hq76qm6r5c5cpcb9zzbxfq4yhhs2fxdxhsyvglz9nhnris4c104", 7444 "depends": ["GenomicRanges", "biomaRt"] 7445 }, 7446 "chromVAR": { 7447 "name": "chromVAR", 7448 "version": "1.32.0", 7449 "sha256": "13yb4ykcapn0i2w1aav3pm3k8yyhfqkibrabd3fzab5gn9kbwwm9", 7450 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "DT", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "Rcpp", "RcppArmadillo", "Rsamtools", "Rtsne", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TFBSTools", "ggplot2", "miniUI", "nabor", "plotly", "shiny"] 7451 }, 7452 "cicero": { 7453 "name": "cicero", 7454 "version": "1.28.0", 7455 "sha256": "1ibxynw77a8mqv9av7z828wcazjpm4sfp83hd412f2rmgkls895x", 7456 "depends": ["Biobase", "BiocGenerics", "FNN", "GenomicRanges", "Gviz", "IRanges", "Matrix", "S4Vectors", "VGAM", "assertthat", "data_table", "dplyr", "ggplot2", "glasso", "igraph", "monocle", "plyr", "reshape2", "stringi", "stringr", "tibble", "tidyr"] 7457 }, 7458 "cigarillo": { 7459 "name": "cigarillo", 7460 "version": "1.0.0", 7461 "sha256": "07ayin3ydibhbv5qxi1bapdw2yf759k3azj57kqvmdpqsdwz1nm9", 7462 "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors"] 7463 }, 7464 "circRNAprofiler": { 7465 "name": "circRNAprofiler", 7466 "version": "1.24.0", 7467 "sha256": "0pq3lxpwb25rkw2g5ykv8xiiq7zppp6r1zyvaykvg8jaaina0mx8", 7468 "depends": ["AnnotationHub", "BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "DESeq2", "GenomeInfoDb", "GenomicRanges", "IRanges", "R_utils", "S4Vectors", "dplyr", "edgeR", "ggplot2", "gwascat", "magrittr", "readr", "reshape2", "rlang", "rtracklayer", "seqinr", "stringi", "stringr", "universalmotif"] 7469 }, 7470 "cleanUpdTSeq": { 7471 "name": "cleanUpdTSeq", 7472 "version": "1.48.0", 7473 "sha256": "1816qqksabhyjzn5kprqmzsqjyq39rgi5kmbylr38ml4idsgw050", 7474 "depends": ["BSgenome", "BSgenome_Drerio_UCSC_danRer7", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "e1071", "seqinr", "stringr"] 7475 }, 7476 "cleaver": { 7477 "name": "cleaver", 7478 "version": "1.48.0", 7479 "sha256": "1xi1n9k40cy7fmizdhjb4cbplpsagqfzfsk26k4zfr6wwwgjphs4", 7480 "depends": ["Biostrings", "IRanges", "S4Vectors"] 7481 }, 7482 "clevRvis": { 7483 "name": "clevRvis", 7484 "version": "1.10.0", 7485 "sha256": "09wlklwpz1bhmm1ca6nxx0a3mzmdxnasn960mnksc7srcpqs4m64", 7486 "depends": ["DT", "R_utils", "colorspace", "colourpicker", "cowplot", "dplyr", "ggiraph", "ggnewscale", "ggplot2", "ggraph", "htmlwidgets", "igraph", "magrittr", "patchwork", "purrr", "readr", "readxl", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinyhelper", "tibble"] 7487 }, 7488 "cliProfiler": { 7489 "name": "cliProfiler", 7490 "version": "1.16.0", 7491 "sha256": "07pzyhwib8mz8bykkygrspyss4ljckj39js60fwig1y0li45b783", 7492 "depends": ["BSgenome", "Biostrings", "GenomicRanges", "S4Vectors", "dplyr", "ggplot2", "rtracklayer"] 7493 }, 7494 "clippda": { 7495 "name": "clippda", 7496 "version": "1.60.0", 7497 "sha256": "10607r90flb2hxfl38mxsrjbgwm551pm7hy8phnffm8g8np0nksl", 7498 "depends": ["Biobase", "lattice", "limma", "rgl", "scatterplot3d", "statmod"] 7499 }, 7500 "clipper": { 7501 "name": "clipper", 7502 "version": "1.50.0", 7503 "sha256": "0ijw8zy19z8l3b4bz0xa412frsmw6jkfjrqbw2yj7cx6sk73hp6y", 7504 "depends": ["Biobase", "KEGGgraph", "Matrix", "Rcpp", "corpcor", "gRbase", "graph", "igraph", "qpgraph"] 7505 }, 7506 "cliqueMS": { 7507 "name": "cliqueMS", 7508 "version": "1.24.0", 7509 "sha256": "03j3xr5bmgs34zb2wq279mjkv4grz6ix9m3azg5d0fmxlndsqqb5", 7510 "depends": ["BH", "MSnbase", "Rcpp", "RcppArmadillo", "coop", "igraph", "matrixStats", "slam", "xcms"] 7511 }, 7512 "clst": { 7513 "name": "clst", 7514 "version": "1.58.0", 7515 "sha256": "0f1l5fgvbqw8mamllqdy2v903vjdd3bpxgprr9ds4zviapwcx5a2", 7516 "depends": ["ROC", "lattice"] 7517 }, 7518 "clstutils": { 7519 "name": "clstutils", 7520 "version": "1.58.0", 7521 "sha256": "0m9wyrndnhq959hqjk6z7cvzr9d50rw2nrzzdndssyjpfhnnkjfi", 7522 "depends": ["RSQLite", "ape", "clst", "lattice", "rjson"] 7523 }, 7524 "clustComp": { 7525 "name": "clustComp", 7526 "version": "1.38.0", 7527 "sha256": "094wp5bf1f521jd7f0pc2w4fvry9vj3w0fx5pr8d9hqph8l60522", 7528 "depends": ["sm"] 7529 }, 7530 "clustSIGNAL": { 7531 "name": "clustSIGNAL", 7532 "version": "1.2.0", 7533 "sha256": "1mydppyp4l5imhmbn833fr94imipcbwlkbx4i2v9r3g1c1gbgf2s", 7534 "depends": ["BiocNeighbors", "BiocParallel", "Matrix", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "bluster", "harmony", "reshape2", "scater"] 7535 }, 7536 "clusterExperiment": { 7537 "name": "clusterExperiment", 7538 "version": "2.30.0", 7539 "sha256": "0lcahnfcld24xjj0fg9xmwapm3pnnf02sgf9gmvp5nkp6pjhmf5p", 7540 "depends": ["BiocGenerics", "BiocSingular", "DelayedArray", "HDF5Array", "Matrix", "NMF", "RColorBrewer", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ape", "cluster", "edgeR", "kernlab", "limma", "locfdr", "matrixStats", "mbkmeans", "phylobase", "pracma", "scales", "stringr", "zinbwave"] 7541 }, 7542 "clusterProfiler": { 7543 "name": "clusterProfiler", 7544 "version": "4.18.0", 7545 "sha256": "1sqxizm5sbjhjyg5kxbb1k1qv1pmldkfa232h04w4z1k4a1isn0l", 7546 "depends": ["AnnotationDbi", "DOSE", "GOSemSim", "GO_db", "dplyr", "enrichplot", "gson", "httr", "igraph", "magrittr", "plyr", "qvalue", "rlang", "tidyr", "yulab_utils"] 7547 }, 7548 "clusterSeq": { 7549 "name": "clusterSeq", 7550 "version": "1.34.0", 7551 "sha256": "1ny2ypmqgwqwqa857bdh19ymizcy6ilk2fzsdbvqm7rh0zwkqnij", 7552 "depends": ["BiocGenerics", "BiocParallel", "baySeq"] 7553 }, 7554 "clusterStab": { 7555 "name": "clusterStab", 7556 "version": "1.82.0", 7557 "sha256": "128ifhm27d0rrj7m6i0ycflv044c9inha3kic4gvyn5ggkmy4fmv", 7558 "depends": ["Biobase"] 7559 }, 7560 "clustifyr": { 7561 "name": "clustifyr", 7562 "version": "1.22.0", 7563 "sha256": "0i8ck3wf61d92fgxg1b3p27xklilibkqz3qavdnmfks2xwzfbs5w", 7564 "depends": ["Matrix", "S4Vectors", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "cowplot", "dplyr", "entropy", "fgsea", "ggplot2", "httr", "matrixStats", "proxy", "rlang", "scales", "stringr", "tibble", "tidyr"] 7565 }, 7566 "cmapR": { 7567 "name": "cmapR", 7568 "version": "1.22.0", 7569 "sha256": "1c8mhspf33byz9mj3zmgf9k2d02g2dv41ick4wka4ghm1x1iygnc", 7570 "depends": ["SummarizedExperiment", "data_table", "flowCore", "matrixStats", "rhdf5"] 7571 }, 7572 "cn_farms": { 7573 "name": "cn.farms", 7574 "version": "1.58.0", 7575 "sha256": "1jm7zwkdhcbsr1i5zc1s35ki0ri3y5mqnpng07h1jvqg9kd15w5f", 7576 "depends": ["Biobase", "DBI", "DNAcopy", "affxparser", "ff", "lattice", "oligo", "oligoClasses", "preprocessCore", "snow"] 7577 }, 7578 "cn_mops": { 7579 "name": "cn.mops", 7580 "version": "1.56.0", 7581 "sha256": "14dihwcwc02p8kcxwisnpq5sv7km5bpyb68v1pnac0pgjxlccn5q", 7582 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo"] 7583 }, 7584 "cnvGSA": { 7585 "name": "cnvGSA", 7586 "version": "1.54.0", 7587 "sha256": "0dmrr4hy1h1v7fa4v2y4wg1i2cf3jq0wldybb0jy0p8q8059gwg8", 7588 "depends": ["GenomicRanges", "brglm", "doParallel", "foreach", "splitstackshape"] 7589 }, 7590 "coGPS": { 7591 "name": "coGPS", 7592 "version": "1.54.0", 7593 "sha256": "0d8611n0ya3b7dnbilakkjjw07mnm0f5vbr58q1kbmvx9v4i0cfz", 7594 "depends": [] 7595 }, 7596 "coMethDMR": { 7597 "name": "coMethDMR", 7598 "version": "1.14.0", 7599 "sha256": "1k0dvlxafam228fbmcs29r2x5zflwwd2ws8q3kbfmjgy2n334159", 7600 "depends": ["AnnotationHub", "BiocParallel", "ExperimentHub", "GenomicRanges", "IRanges", "bumphunter", "lmerTest"] 7601 }, 7602 "coRdon": { 7603 "name": "coRdon", 7604 "version": "1.28.0", 7605 "sha256": "0vkg3pch29mkab684mmbbrvpk2w1lkj4kfda75i50wy10x706cnv", 7606 "depends": ["Biobase", "Biostrings", "data_table", "dplyr", "ggplot2", "purrr", "stringr"] 7607 }, 7608 "codelink": { 7609 "name": "codelink", 7610 "version": "1.78.0", 7611 "sha256": "01mkh2mvgaiq760ga379m9s0wapv0g8bkmjm0c1wxc4bay6hgbph", 7612 "depends": ["Biobase", "BiocGenerics", "annotate", "limma"] 7613 }, 7614 "cogena": { 7615 "name": "cogena", 7616 "version": "1.44.0", 7617 "sha256": "1klqysglaz37lyy3aj99fpddw9nz9k06473qg6lhvjrpfgbr1chf", 7618 "depends": ["Biobase", "amap", "apcluster", "biwt", "class", "cluster", "corrplot", "devtools", "doParallel", "dplyr", "fastcluster", "foreach", "ggplot2", "gplots", "kohonen", "mclust", "reshape2", "stringr", "tibble", "tidyr"] 7619 }, 7620 "cogeqc": { 7621 "name": "cogeqc", 7622 "version": "1.14.0", 7623 "sha256": "19fyg5na5g30vp62ki8hxb0pg24k6dzd08xan7f7biqh0ygc2ig5", 7624 "depends": ["Biostrings", "ggbeeswarm", "ggplot2", "ggtree", "igraph", "jsonlite", "patchwork", "reshape2", "rlang", "scales"] 7625 }, 7626 "cola": { 7627 "name": "cola", 7628 "version": "2.16.0", 7629 "sha256": "1h6w44nbach8wvnd3qjs107fmcqn3wzpqv587c651xqcjrq6d1w7", 7630 "depends": ["BiocGenerics", "ComplexHeatmap", "GetoptLong", "GlobalOptions", "RColorBrewer", "Rcpp", "brew", "circlize", "clue", "cluster", "crayon", "digest", "doParallel", "doRNG", "eulerr", "foreach", "httr", "impute", "irlba", "knitr", "markdown", "matrixStats", "mclust", "microbenchmark", "png", "skmeans", "xml2"] 7631 }, 7632 "combi": { 7633 "name": "combi", 7634 "version": "1.22.0", 7635 "sha256": "1miy20axfip09v4ma5v70knv1h118w0rmdssqbzam2dxbdilipcp", 7636 "depends": ["BB", "Biobase", "DBI", "Matrix", "SummarizedExperiment", "alabama", "cobs", "ggplot2", "limma", "nleqslv", "phyloseq", "reshape2", "tensor", "vegan"] 7637 }, 7638 "compEpiTools": { 7639 "name": "compEpiTools", 7640 "version": "1.44.0", 7641 "sha256": "0j35bq78pz79413149j0j4g4mz05kmyzcbpg6wgq04c9xyjnkyzv", 7642 "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "GO_db", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "XVector", "gplots", "methylPipe", "topGO"] 7643 }, 7644 "compSPOT": { 7645 "name": "compSPOT", 7646 "version": "1.8.0", 7647 "sha256": "1ab63jhw8la182irpygpzdasn71d24y1bwabn834h3sw1h0jnxg2", 7648 "depends": ["data_table", "ggplot2", "ggpubr", "gridExtra", "magrittr", "plotly"] 7649 }, 7650 "compcodeR": { 7651 "name": "compcodeR", 7652 "version": "1.46.0", 7653 "sha256": "16i81f8i9g1f6cwk96idzr377p45s23s1d018x8aiacs92c1kfxv", 7654 "depends": ["KernSmooth", "MASS", "ROCR", "ape", "caTools", "edgeR", "ggplot2", "gplots", "gtools", "knitr", "lattice", "limma", "markdown", "matrixStats", "modeest", "phylolm", "rmarkdown", "shiny", "shinydashboard", "sm", "stringr", "vioplot"] 7655 }, 7656 "concordexR": { 7657 "name": "concordexR", 7658 "version": "1.10.0", 7659 "sha256": "03xrjkgsqcd9p7029vlif5bgcbpf5yzf03dg3cni8rf9a4sgrh9y", 7660 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "DelayedArray", "Matrix", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "bluster", "cli", "purrr", "rlang", "sparseMatrixStats"] 7661 }, 7662 "condiments": { 7663 "name": "condiments", 7664 "version": "1.18.0", 7665 "sha256": "1rld3jllr8iax3ivb20cg5syzvci75g53r8g86ac76r95sqbsdi4", 7666 "depends": ["BiocParallel", "Ecume", "RANN", "SingleCellExperiment", "SummarizedExperiment", "TrajectoryUtils", "distinct", "dplyr", "igraph", "magrittr", "matrixStats", "mgcv", "pbapply", "slingshot"] 7667 }, 7668 "consICA": { 7669 "name": "consICA", 7670 "version": "2.8.0", 7671 "sha256": "0l54a4iyyykwy1zg8mjk87swjbsfjcs4jbyqicpci377wa2fcpvj", 7672 "depends": ["BiocParallel", "GO_db", "Rfast", "SummarizedExperiment", "fastICA", "ggplot2", "graph", "org_Hs_eg_db", "pheatmap", "sm", "survival", "topGO"] 7673 }, 7674 "consensus": { 7675 "name": "consensus", 7676 "version": "1.28.0", 7677 "sha256": "14wzl0vpgxf34ab6f3ymrhy19rvn9s54zx9d4fqs4wsmzgw6r4dl", 7678 "depends": ["RColorBrewer", "gplots", "matrixStats"] 7679 }, 7680 "consensusDE": { 7681 "name": "consensusDE", 7682 "version": "1.28.0", 7683 "sha256": "1rflkdj8kkb0vhhhlyfirpvkqanbxgfjqwi7diyr35rhkfynra4y", 7684 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "EDASeq", "EnsDb_Hsapiens_v86", "GenomicAlignments", "GenomicFeatures", "RColorBrewer", "RUVSeq", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TxDb_Dmelanogaster_UCSC_dm3_ensGene", "airway", "data_table", "dendextend", "edgeR", "ensembldb", "limma", "org_Hs_eg_db", "pcaMethods"] 7685 }, 7686 "consensusOV": { 7687 "name": "consensusOV", 7688 "version": "1.32.0", 7689 "sha256": "08k9x2alip4yz8243fnakjrp7awv68d6wa4rlbnwbnsp3dx3pdqy", 7690 "depends": ["Biobase", "BiocParallel", "GSVA", "gdata", "genefu", "limma", "matrixStats", "randomForest"] 7691 }, 7692 "consensusSeekeR": { 7693 "name": "consensusSeekeR", 7694 "version": "1.38.0", 7695 "sha256": "04s65v7cg7mzyarym98b2qn5gm61z96yq538cxvglc6bsgn0kglq", 7696 "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "rtracklayer", "stringr"] 7697 }, 7698 "conumee": { 7699 "name": "conumee", 7700 "version": "1.44.0", 7701 "sha256": "1v3xxc4z8d98gyhy4q3mbdi40mjw8k44r1328mqpikgyrn2l2rp5", 7702 "depends": ["DNAcopy", "GenomicRanges", "IRanges", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno_ilm10b2_hg19", "IlluminaHumanMethylationEPICmanifest", "Seqinfo", "minfi", "rtracklayer"] 7703 }, 7704 "convert": { 7705 "name": "convert", 7706 "version": "1.86.0", 7707 "sha256": "0y3932nyp4fdp4yjnzskg1cg4rsg0yc36cl5qqrj2svxh5d4s7b8", 7708 "depends": ["Biobase", "limma", "marray"] 7709 }, 7710 "copa": { 7711 "name": "copa", 7712 "version": "1.78.0", 7713 "sha256": "08r4yx0jqlsm4h6c2aafdqlrm4pa4zyyrq8n5ygkf5j738sis7k1", 7714 "depends": ["Biobase"] 7715 }, 7716 "corral": { 7717 "name": "corral", 7718 "version": "1.20.0", 7719 "sha256": "1njbbbnzlpp4m30ls2b6ff9fdwacjdnplh39115ix2lxnbcyg7np", 7720 "depends": ["Matrix", "MultiAssayExperiment", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggthemes", "gridExtra", "irlba", "pals", "reshape2", "transport"] 7721 }, 7722 "coseq": { 7723 "name": "coseq", 7724 "version": "1.34.0", 7725 "sha256": "1mfndl9gzfpf8gv9qszaa8fy2ma9nmc1d1lb66j9y8v8xj9yk9vw", 7726 "depends": ["BiocParallel", "DESeq2", "HTSCluster", "HTSFilter", "Rmixmod", "S4Vectors", "SummarizedExperiment", "capushe", "compositions", "corrplot", "e1071", "edgeR", "ggplot2", "mvtnorm", "scales"] 7727 }, 7728 "cosmiq": { 7729 "name": "cosmiq", 7730 "version": "1.44.0", 7731 "sha256": "1a70a6kl5k0a6l8ihhlyvjscr8srvgy2qljf8h8j5cm8pgiljyzl", 7732 "depends": ["MassSpecWavelet", "Rcpp", "faahKO", "pracma", "xcms"] 7733 }, 7734 "cosmosR": { 7735 "name": "cosmosR", 7736 "version": "1.18.0", 7737 "sha256": "0l816srg6rgmb53ws45vwv3w8bvlyh8qcyz1q2drz9fg0w93645b", 7738 "depends": ["CARNIVAL", "GSEABase", "decoupleR", "dorothea", "dplyr", "igraph", "progress", "purrr", "rlang", "stringr", "visNetwork"] 7739 }, 7740 "countsimQC": { 7741 "name": "countsimQC", 7742 "version": "1.28.0", 7743 "sha256": "0kbcl53mi9ch3d336xccw500bvghjy6lify8jpj7hmnx7bxhzzlq", 7744 "depends": ["DESeq2", "DT", "GenomeInfoDbData", "SummarizedExperiment", "caTools", "dplyr", "edgeR", "genefilter", "ggplot2", "ragg", "randtests", "rmarkdown", "tidyr"] 7745 }, 7746 "covEB": { 7747 "name": "covEB", 7748 "version": "1.36.0", 7749 "sha256": "05glwld2sl0fcd1xgq20yc7pjs91i814ca5h2y2mjj55160l44ks", 7750 "depends": ["Biobase", "LaplacesDemon", "Matrix", "gsl", "igraph", "mvtnorm"] 7751 }, 7752 "covRNA": { 7753 "name": "covRNA", 7754 "version": "1.36.0", 7755 "sha256": "1marp993hl0in7n68awlynpyczzbnwy6rgvilf5c52bqrp6hz40w", 7756 "depends": ["Biobase", "ade4", "genefilter"] 7757 }, 7758 "cpvSNP": { 7759 "name": "cpvSNP", 7760 "version": "1.42.0", 7761 "sha256": "14vb6rj7z633dgkdlacv5zjmqdfphi4lhs2gfl41x34ppz8z8fy3", 7762 "depends": ["BiocParallel", "GSEABase", "GenomicFeatures", "corpcor", "ggplot2", "plyr"] 7763 }, 7764 "cqn": { 7765 "name": "cqn", 7766 "version": "1.56.0", 7767 "sha256": "0aj0g8j4qgfvf421iyxq2w44jp3ryl3pcazrq1qslf48rgndf3kd", 7768 "depends": ["mclust", "nor1mix", "quantreg"] 7769 }, 7770 "crisprBase": { 7771 "name": "crisprBase", 7772 "version": "1.14.0", 7773 "sha256": "17rimskjajjh55pybyk145ag52nqnpxfm1k88xm631j0r4bg51vf", 7774 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "stringr"] 7775 }, 7776 "crisprBowtie": { 7777 "name": "crisprBowtie", 7778 "version": "1.14.0", 7779 "sha256": "1d1spfnfr3z3pqwq077j6pjind9j6vi82y2cmla0llfidb2gychv", 7780 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "Rbowtie", "Seqinfo", "crisprBase", "readr", "stringr"] 7781 }, 7782 "crisprBwa": { 7783 "name": "crisprBwa", 7784 "version": "1.14.0", 7785 "sha256": "0mh9vixbmny6ifgc20381y7hajf1cda3scyvc0sbij0f70b83hcr", 7786 "depends": ["BSgenome", "BiocGenerics", "Rbwa", "Seqinfo", "crisprBase", "readr", "stringr"] 7787 }, 7788 "crisprDesign": { 7789 "name": "crisprDesign", 7790 "version": "1.12.0", 7791 "sha256": "1cgqd6maqk2ij852n4ajpmc0kz36ap1614yi0q1x3rnyp427p2mp", 7792 "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "S4Vectors", "Seqinfo", "VariantAnnotation", "crisprBase", "crisprBowtie", "crisprScore", "rtracklayer", "txdbmaker"] 7793 }, 7794 "crisprScore": { 7795 "name": "crisprScore", 7796 "version": "1.14.0", 7797 "sha256": "1vzdiz0gz5fbrn0sak3gylaxgxavyb1qcx7ldg02mkvhd2mlbcx8", 7798 "depends": ["BiocGenerics", "Biostrings", "IRanges", "XVector", "basilisk", "crisprScoreData", "randomForest", "reticulate", "stringr"] 7799 }, 7800 "crisprShiny": { 7801 "name": "crisprShiny", 7802 "version": "1.6.0", 7803 "sha256": "0vvdmfzvxva41fln61nd2l3chf9nvg9rcgrxwd8zgpm9gh84f9sb", 7804 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "DT", "S4Vectors", "Seqinfo", "crisprBase", "crisprDesign", "crisprScore", "crisprViz", "htmlwidgets", "pwalign", "shiny", "shinyBS", "shinyjs", "waiter"] 7805 }, 7806 "crisprVerse": { 7807 "name": "crisprVerse", 7808 "version": "1.12.0", 7809 "sha256": "0z3d1sqhp15y0k1i0pkbzil60gn6hfsgm91yj6kci79axslia40l", 7810 "depends": ["BiocManager", "cli", "crisprBase", "crisprBowtie", "crisprDesign", "crisprScore", "crisprScoreData", "crisprViz", "rlang"] 7811 }, 7812 "crisprViz": { 7813 "name": "crisprViz", 7814 "version": "1.12.0", 7815 "sha256": "1h3qnndqj1561fhayzmg734ixflwcgwrxv0a2k7zqwbgmbpq73qy", 7816 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "S4Vectors", "Seqinfo", "crisprBase", "crisprDesign", "txdbmaker"] 7817 }, 7818 "crlmm": { 7819 "name": "crlmm", 7820 "version": "1.68.0", 7821 "sha256": "0fpyn0q596k7yb03y10dcrrbn8narngca97sj1dldij0l07100mw", 7822 "depends": ["Biobase", "BiocGenerics", "RcppEigen", "VGAM", "affyio", "beanplot", "ellipse", "ff", "foreach", "illuminaio", "lattice", "limma", "matrixStats", "mvtnorm", "oligoClasses", "preprocessCore"] 7823 }, 7824 "crumblr": { 7825 "name": "crumblr", 7826 "version": "1.2.0", 7827 "sha256": "0fcwl1cql812z22h4qmr1piyaa10k38zgyba18nz9xf9cin385c2", 7828 "depends": ["MASS", "Rdpack", "Rfast", "SingleCellExperiment", "dplyr", "ggplot2", "ggtree", "tidytree", "variancePartition", "viridis"] 7829 }, 7830 "crupR": { 7831 "name": "crupR", 7832 "version": "1.2.0", 7833 "sha256": "1ffvljw9q9m5405k9r9y409cnl64j897kwz3qmp2hcspmlq9mrs7", 7834 "depends": ["BiocParallel", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "TxDb_Mmusculus_UCSC_mm9_knownGene", "bamsignals", "dplyr", "fs", "ggplot2", "magrittr", "matrixStats", "preprocessCore", "randomForest", "reshape2", "rtracklayer"] 7835 }, 7836 "csaw": { 7837 "name": "csaw", 7838 "version": "1.44.0", 7839 "sha256": "10pk3lmjjmdyfp10fcnjbgfcxzlkd1fbjvh0h53ycq37p6sa49qb", 7840 "depends": ["BiocGenerics", "BiocParallel", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "edgeR", "limma", "metapod"] 7841 }, 7842 "csdR": { 7843 "name": "csdR", 7844 "version": "1.16.0", 7845 "sha256": "08ryx2jczvn7x9vl965adqpkhpbhbbc3rhj30mhrpgl45jbn7bka", 7846 "depends": ["Rcpp", "RhpcBLASctl", "WGCNA", "glue", "matrixStats"] 7847 }, 7848 "ctc": { 7849 "name": "ctc", 7850 "version": "1.84.0", 7851 "sha256": "0h5lnb3bb88f6cbw38jn9rp6mynx8x7jzini2i9b8jw9myc2g6sx", 7852 "depends": ["amap"] 7853 }, 7854 "ctsGE": { 7855 "name": "ctsGE", 7856 "version": "1.36.0", 7857 "sha256": "19qw1ww4nxplqnjyca8lcx1mqzfx9j664rnw6pprlpfsc5c5kg4c", 7858 "depends": ["ccaPP", "ggplot2", "limma", "reshape2", "shiny", "stringr"] 7859 }, 7860 "customCMPdb": { 7861 "name": "customCMPdb", 7862 "version": "1.20.0", 7863 "sha256": "19s36a2j7gr7563rgblgwmdym28har666m28ci377bm6hb25aky8", 7864 "depends": ["AnnotationHub", "BiocFileCache", "ChemmineR", "RSQLite", "XML", "rappdirs"] 7865 }, 7866 "cyanoFilter": { 7867 "name": "cyanoFilter", 7868 "version": "1.18.0", 7869 "sha256": "1m1lgg7gydzhk01vp0ddgsnn5rkdc47f0ippy5shh1l9mfj8fpah", 7870 "depends": ["Biobase", "GGally", "cytometree", "flowClust", "flowCore", "flowDensity", "ggplot2", "mrfDepth"] 7871 }, 7872 "cycle": { 7873 "name": "cycle", 7874 "version": "1.64.0", 7875 "sha256": "1kaz4azy4gns1sww7n4wxa1kmlj8crk01lgvb15rlkcg38if9xma", 7876 "depends": ["Biobase", "Mfuzz"] 7877 }, 7878 "cydar": { 7879 "name": "cydar", 7880 "version": "1.34.0", 7881 "sha256": "1wv5y5v4x3r84h1sh43zl841wxqnv9ffspr8nm6lypncpg99qdqw", 7882 "depends": ["Biobase", "BiocGenerics", "BiocNeighbors", "BiocParallel", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "flowCore", "shiny", "viridis"] 7883 }, 7884 "cypress": { 7885 "name": "cypress", 7886 "version": "1.6.0", 7887 "sha256": "1f1kh5789rmpz3v35ldbgmjc39r5swlfhfciir4qcmkpi7gk23q4", 7888 "depends": ["BiocParallel", "DESeq2", "MASS", "PROPER", "RColorBrewer", "SummarizedExperiment", "TCA", "TOAST", "abind", "checkmate", "dplyr", "e1071", "edgeR", "mvtnorm", "preprocessCore", "rlang", "sirt", "tibble"] 7889 }, 7890 "cytoKernel": { 7891 "name": "cytoKernel", 7892 "version": "1.16.0", 7893 "sha256": "1bazyy554vk2lwdvs612g2qjxgbnqgv0pyj0w1jyxlvh992x91nh", 7894 "depends": ["BiocParallel", "ComplexHeatmap", "Rcpp", "S4Vectors", "SummarizedExperiment", "ashr", "circlize", "data_table", "dplyr", "magrittr", "rlang"] 7895 }, 7896 "cytoMEM": { 7897 "name": "cytoMEM", 7898 "version": "1.14.0", 7899 "sha256": "0h122sdnv5ivmb7awsz20cqi6k1wgb9v84mpd938igacnrv6d95a", 7900 "depends": ["flowCore", "gplots", "matrixStats"] 7901 }, 7902 "cytolib": { 7903 "name": "cytolib", 7904 "version": "2.22.0", 7905 "sha256": "0qfh5srgdz01n66p9midq0051hl83dhzrkm0mvqlzs7ccm9xvb70", 7906 "depends": ["BH", "RProtoBufLib", "Rhdf5lib"] 7907 }, 7908 "cytomapper": { 7909 "name": "cytomapper", 7910 "version": "1.22.0", 7911 "sha256": "1r68fbhwgnhplp3mmkcnga4kxwx8yj9c7vldwzxacpbihw4hxi92", 7912 "depends": ["BiocParallel", "DelayedArray", "EBImage", "HDF5Array", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "ggbeeswarm", "ggplot2", "matrixStats", "nnls", "raster", "rhdf5", "shiny", "shinydashboard", "svgPanZoom", "svglite", "viridis"] 7913 }, 7914 "cytoviewer": { 7915 "name": "cytoviewer", 7916 "version": "1.10.0", 7917 "sha256": "0lx73ldfyy2s3dkh13ph8pqs003fg07yjjfqn1m3l5z9hxgcnzmk", 7918 "depends": ["EBImage", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "archive", "colourpicker", "cytomapper", "shiny", "shinycssloaders", "shinydashboard", "svgPanZoom", "svglite", "viridis"] 7919 }, 7920 "dStruct": { 7921 "name": "dStruct", 7922 "version": "1.16.0", 7923 "sha256": "1mifjcjgihr4gsshx1197x5wq87xyqwl38dmkb2pqppvf3ma2ppm", 7924 "depends": ["IRanges", "S4Vectors", "ggplot2", "purrr", "reshape2", "rlang", "zoo"] 7925 }, 7926 "daMA": { 7927 "name": "daMA", 7928 "version": "1.82.0", 7929 "sha256": "1klyw8f3b15160q9qdaqd6dp50l6xvwp1qgyphamwj6wh0y64xqg", 7930 "depends": ["MASS"] 7931 }, 7932 "dada2": { 7933 "name": "dada2", 7934 "version": "1.38.0", 7935 "sha256": "0dcb37hv4wa6qz0f0xqmiw7n938lkm4dp9n9ardhwf633qcsn00d", 7936 "depends": ["BiocGenerics", "Biostrings", "IRanges", "Rcpp", "RcppParallel", "ShortRead", "XVector", "ggplot2", "reshape2"] 7937 }, 7938 "dagLogo": { 7939 "name": "dagLogo", 7940 "version": "1.48.0", 7941 "sha256": "0cb5yqfjgy3qxnqbppavfifgmk2gys8yww200kqpgkkwn4wdw81k", 7942 "depends": ["BiocGenerics", "Biostrings", "UniProt_ws", "biomaRt", "httr", "motifStack", "pheatmap"] 7943 }, 7944 "dar": { 7945 "name": "dar", 7946 "version": "1.6.0", 7947 "sha256": "0dxpd19pqkqxpb6r9fzb068a4saspzasx5i171inib4jq7r6yicx", 7948 "depends": ["ComplexHeatmap", "UpSetR", "cli", "crayon", "dplyr", "generics", "ggplot2", "glue", "gplots", "heatmaply", "magrittr", "mia", "phyloseq", "purrr", "readr", "rlang", "scales", "stringr", "tibble", "tidyr", "waldo"] 7949 }, 7950 "dcGSA": { 7951 "name": "dcGSA", 7952 "version": "1.38.0", 7953 "sha256": "1dfnchgyiw7g424s24jshzcz56whdpxbzsapyw4bna0ldhd0m4mp", 7954 "depends": ["BiocParallel", "Matrix"] 7955 }, 7956 "dcanr": { 7957 "name": "dcanr", 7958 "version": "1.26.0", 7959 "sha256": "0ga220j0na7biwrwxhzdjw0qv8624lcw05c5kagjd889rf27sizj", 7960 "depends": ["Matrix", "RColorBrewer", "circlize", "doRNG", "foreach", "igraph", "plyr", "reshape2", "stringr"] 7961 }, 7962 "ddCt": { 7963 "name": "ddCt", 7964 "version": "1.66.0", 7965 "sha256": "0xl3034xixqms5q66glbc3c697fff1dd5qyn57pm4jbyn6gfrsrw", 7966 "depends": ["Biobase", "BiocGenerics", "RColorBrewer", "lattice", "xtable"] 7967 }, 7968 "ddPCRclust": { 7969 "name": "ddPCRclust", 7970 "version": "1.30.0", 7971 "sha256": "1vj6a3wd4r0w606cm6pkdxgmmq0cmibly1xs9fdnli8z6sxpnqn1", 7972 "depends": ["R_utils", "SamSPECTRAL", "clue", "flowCore", "flowDensity", "flowPeaks", "ggplot2", "openxlsx", "plotrix"] 7973 }, 7974 "dearseq": { 7975 "name": "dearseq", 7976 "version": "1.22.0", 7977 "sha256": "04a4ifz73bz0ivqirwzcr1aqfwbm7k63d9qic26n418xrdk9liwz", 7978 "depends": ["CompQuadForm", "KernSmooth", "dplyr", "ggplot2", "magrittr", "matrixStats", "patchwork", "pbapply", "reshape2", "rlang", "scattermore", "statmod", "survey", "tibble", "viridisLite"] 7979 }, 7980 "debrowser": { 7981 "name": "debrowser", 7982 "version": "1.38.0", 7983 "sha256": "0d90w8v43psm2z47i1np20jvy6l331n18wyzngqgk94g7qcacw98", 7984 "depends": ["AnnotationDbi", "DESeq2", "DOSE", "DT", "GenomicRanges", "Harman", "IRanges", "RColorBrewer", "RCurl", "S4Vectors", "SummarizedExperiment", "annotate", "apeglm", "ashr", "clusterProfiler", "colourpicker", "edgeR", "enrichplot", "ggplot2", "gplots", "heatmaply", "igraph", "jsonlite", "limma", "org_Hs_eg_db", "org_Mm_eg_db", "pathview", "plotly", "reshape2", "shiny", "shinyBS", "shinydashboard", "shinyjs", "stringi", "sva"] 7985 }, 7986 "decompTumor2Sig": { 7987 "name": "decompTumor2Sig", 7988 "version": "2.26.0", 7989 "sha256": "1qrgc6s3fidcjg1j16ndg9l3awh0ga2v3j84b6yg8d52whf9xs0a", 7990 "depends": ["BSgenome_Hsapiens_UCSC_hg19", "BiocGenerics", "Biostrings", "GenomicFeatures", "GenomicRanges", "Matrix", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "VariantAnnotation", "data_table", "ggplot2", "ggseqlogo", "gridExtra", "plyr", "quadprog", "readxl"] 7991 }, 7992 "decontX": { 7993 "name": "decontX", 7994 "version": "1.8.0", 7995 "sha256": "00w0xd9i6lhb84q7mjjy1wgrs4sb20hpjxmkfkymk2apf5azf9p7", 7996 "depends": ["BH", "DelayedArray", "MCMCprecision", "Matrix", "Rcpp", "RcppEigen", "RcppParallel", "S4Vectors", "Seurat", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "celda", "dbscan", "ggplot2", "patchwork", "plyr", "reshape2", "rstan", "rstantools", "scater", "withr"] 7997 }, 7998 "decontam": { 7999 "name": "decontam", 8000 "version": "1.30.0", 8001 "sha256": "0vf4rkw66qxg8rcpicr0pjpgrg377nd0ykizzx5hym9vj84jhcwl", 8002 "depends": ["ggplot2", "reshape2"] 8003 }, 8004 "deconvR": { 8005 "name": "deconvR", 8006 "version": "1.16.0", 8007 "sha256": "0nbkic26yw1gwcn2ha2jb4hjinc0id0gjhwl59lf38aiy9ckssya", 8008 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "assertthat", "data_table", "dplyr", "e1071", "foreach", "magrittr", "matrixStats", "methylKit", "minfi", "nnls", "quadprog", "rsq", "tidyr"] 8009 }, 8010 "decoupleR": { 8011 "name": "decoupleR", 8012 "version": "2.16.0", 8013 "sha256": "1wg6nkjzj30lddhz95d1mlmdlr3fvpwkamzyil23wzm2yz6yw4i4", 8014 "depends": ["BiocParallel", "Matrix", "broom", "dplyr", "magrittr", "parallelly", "purrr", "rlang", "stringr", "tibble", "tidyr", "tidyselect", "withr"] 8015 }, 8016 "deepSNV": { 8017 "name": "deepSNV", 8018 "version": "1.56.0", 8019 "sha256": "0dl4d5w2s25j8gfrrbc6gm2jz8jss89dcs6k0w2lwfh88m6h6lr4", 8020 "depends": ["Biostrings", "GenomicRanges", "IRanges", "Rhtslib", "SummarizedExperiment", "VGAM", "VariantAnnotation"] 8021 }, 8022 "deltaCaptureC": { 8023 "name": "deltaCaptureC", 8024 "version": "1.24.0", 8025 "sha256": "06d8ml983s4l033vwnjh5sj8hz283zfrdkpfqj0z8nwm35vnq39j", 8026 "depends": ["DESeq2", "GenomicRanges", "IRanges", "SummarizedExperiment", "ggplot2", "tictoc"] 8027 }, 8028 "deltaGseg": { 8029 "name": "deltaGseg", 8030 "version": "1.50.0", 8031 "sha256": "0y7i05l2lbv2dnib5d069zrdhmr432ig4fj72p4w72mzizfmm7p9", 8032 "depends": ["changepoint", "fBasics", "ggplot2", "pvclust", "reshape", "scales", "tseries", "wavethresh"] 8033 }, 8034 "demuxSNP": { 8035 "name": "demuxSNP", 8036 "version": "1.8.0", 8037 "sha256": "1jshg2rqmlw59cdha9k4zzrhp2z4kl8hqgb00h31khi296nrbv79", 8038 "depends": ["BiocGenerics", "IRanges", "KernelKnn", "Matrix", "MatrixGenerics", "Seqinfo", "SingleCellExperiment", "SummarizedExperiment", "VariantAnnotation", "class", "demuxmix", "dplyr", "ensembldb"] 8039 }, 8040 "demuxmix": { 8041 "name": "demuxmix", 8042 "version": "1.12.0", 8043 "sha256": "0p5l2ig6kwn87ksckrxf10f8cm0x7c6a07hpsn79a50jmidch902", 8044 "depends": ["MASS", "Matrix", "ggplot2", "gridExtra"] 8045 }, 8046 "densvis": { 8047 "name": "densvis", 8048 "version": "1.20.0", 8049 "sha256": "1pp5ivc9rb40c66p74ypn6w2jx0maj64205rbb5k2xf70592i2p4", 8050 "depends": ["Rcpp", "Rtsne", "assertthat", "basilisk", "irlba", "reticulate"] 8051 }, 8052 "derfinder": { 8053 "name": "derfinder", 8054 "version": "1.44.0", 8055 "sha256": "19r6bzx6lz03pvzjvvy0g6pbf48vzp229lbd2lpgp3z6x1ncrrz5", 8056 "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "Hmisc", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "bumphunter", "derfinderHelper", "qvalue", "rtracklayer"] 8057 }, 8058 "derfinderHelper": { 8059 "name": "derfinderHelper", 8060 "version": "1.44.0", 8061 "sha256": "0ppgqsrrkizxzkq0bycx05wdmf3j6l3hmyp8x4is0k36s3x5x7kn", 8062 "depends": ["IRanges", "Matrix", "S4Vectors"] 8063 }, 8064 "derfinderPlot": { 8065 "name": "derfinderPlot", 8066 "version": "1.44.0", 8067 "sha256": "1kh8snbldzxvs9n2i35dd1361hxnv8rwm0ll36kjywldlaa27bkj", 8068 "depends": ["GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "Seqinfo", "derfinder", "ggbio", "ggplot2", "limma", "plyr", "reshape2", "scales"] 8069 }, 8070 "diffGeneAnalysis": { 8071 "name": "diffGeneAnalysis", 8072 "version": "1.92.0", 8073 "sha256": "1h9qsnj69xpzcrsx9pkf8bxinhpc08zmb5ykx7v339sghkvnqzn4", 8074 "depends": ["minpack_lm"] 8075 }, 8076 "diffHic": { 8077 "name": "diffHic", 8078 "version": "1.42.0", 8079 "sha256": "08bxncp88k15sj0xfhw9fsv9kk3g4f56qqp6ybrqq1ys64b56a3z", 8080 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "SummarizedExperiment", "csaw", "edgeR", "limma", "locfit", "rhdf5", "rtracklayer"] 8081 }, 8082 "diffUTR": { 8083 "name": "diffUTR", 8084 "version": "1.18.0", 8085 "sha256": "00dprqbngf41n5yncaxn0kkfq0dxgz9df6c8p9064k3z35bsn5si", 8086 "depends": ["ComplexHeatmap", "DEXSeq", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsubread", "S4Vectors", "SummarizedExperiment", "dplyr", "edgeR", "ensembldb", "ggplot2", "ggrepel", "limma", "matrixStats", "rtracklayer", "stringi", "viridisLite"] 8087 }, 8088 "diffcoexp": { 8089 "name": "diffcoexp", 8090 "version": "1.30.0", 8091 "sha256": "010hjbsk0y2gdk543jsjdykyd01141fmqn3pl57adhsgxmxcr8pp", 8092 "depends": ["BiocGenerics", "DiffCorr", "SummarizedExperiment", "WGCNA", "igraph", "psych"] 8093 }, 8094 "diffcyt": { 8095 "name": "diffcyt", 8096 "version": "1.30.0", 8097 "sha256": "13rz4dp034pm7273z1ngrl58fqlaziv8qn501jhg3hwkjclbfzhv", 8098 "depends": ["ComplexHeatmap", "FlowSOM", "S4Vectors", "SummarizedExperiment", "circlize", "dplyr", "edgeR", "flowCore", "limma", "lme4", "magrittr", "multcomp", "reshape2", "tidyr"] 8099 }, 8100 "diffuStats": { 8101 "name": "diffuStats", 8102 "version": "1.30.0", 8103 "sha256": "1hq9j64lrk6f0xskz8jn1s5ddkr947y6clj94ylkan0i68gbbpzn", 8104 "depends": ["MASS", "Matrix", "Rcpp", "RcppArmadillo", "RcppParallel", "checkmate", "expm", "igraph", "plyr", "precrec"] 8105 }, 8106 "diggit": { 8107 "name": "diggit", 8108 "version": "1.42.0", 8109 "sha256": "1xi6rczrvky4s3xdb8dngadrm2iz5xj3mli869b0bn0ggsw735z0", 8110 "depends": ["Biobase", "ks", "viper"] 8111 }, 8112 "dinoR": { 8113 "name": "dinoR", 8114 "version": "1.6.0", 8115 "sha256": "052lxngxi2pkxamppvafmczdxgviz7la2mbkf2jz0fa3f0di3czv", 8116 "depends": ["BiocGenerics", "ComplexHeatmap", "GenomicRanges", "Matrix", "SummarizedExperiment", "circlize", "cowplot", "dplyr", "edgeR", "ggplot2", "rlang", "stringr", "tibble", "tidyr", "tidyselect"] 8117 }, 8118 "dir_expiry": { 8119 "name": "dir.expiry", 8120 "version": "1.18.0", 8121 "sha256": "1hgd5raxj732z0y5irb7vszcxf8xfha23rs3fi1jwjc84dxkghvi", 8122 "depends": ["filelock"] 8123 }, 8124 "discordant": { 8125 "name": "discordant", 8126 "version": "1.34.0", 8127 "sha256": "07x2ck5vnb1nyk0lz1ffpgkfdas3x4p3fpw0zb7msvvpw9ny34jv", 8128 "depends": ["Biobase", "MASS", "Rcpp", "biwt", "dplyr", "gtools"] 8129 }, 8130 "distinct": { 8131 "name": "distinct", 8132 "version": "1.22.0", 8133 "sha256": "0cpdszswk06pc0cyb51lmi4xrdcjxzadzkvj34y62i3fghfzhzxa", 8134 "depends": ["Matrix", "Rcpp", "RcppArmadillo", "SingleCellExperiment", "SummarizedExperiment", "doParallel", "doRNG", "foreach", "ggplot2", "limma", "scater"] 8135 }, 8136 "dittoSeq": { 8137 "name": "dittoSeq", 8138 "version": "1.22.0", 8139 "sha256": "0fb5c78r3qi8px398fcwqkisxdx5cz6afz1plrgr3z1fdcxnspqz", 8140 "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "colorspace", "cowplot", "ggplot2", "ggrepel", "ggridges", "gridExtra", "pheatmap", "reshape2"] 8141 }, 8142 "divergence": { 8143 "name": "divergence", 8144 "version": "1.26.0", 8145 "sha256": "0xahfjc5pclrq4m41z56ysyv83n8smw2jfv53312akcy8i16wbi7", 8146 "depends": ["SummarizedExperiment"] 8147 }, 8148 "dks": { 8149 "name": "dks", 8150 "version": "1.56.0", 8151 "sha256": "1zhzcq6jgcnl8di11804d6b3z5jb077cg1p3rhilpzlqsww02ym8", 8152 "depends": ["cubature"] 8153 }, 8154 "dmGsea": { 8155 "name": "dmGsea", 8156 "version": "1.0.0", 8157 "sha256": "1cykkajxdsb7ama3afffc9fjhfvfci1xs7j6849l5c4lqd41v3kw", 8158 "depends": ["AnnotationDbi", "BiasedUrn", "Matrix", "Seqinfo", "SummarizedExperiment", "dqrng", "poolr"] 8159 }, 8160 "dmrseq": { 8161 "name": "dmrseq", 8162 "version": "1.30.0", 8163 "sha256": "03a5my4a8dja3lnrdzng7554rfkymcvdgixibhx57hqkwwvj4qcj", 8164 "depends": ["AnnotationHub", "BiocParallel", "DelayedMatrixStats", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "Seqinfo", "annotatr", "bsseq", "bumphunter", "ggplot2", "locfit", "matrixStats", "nlme", "outliers", "rtracklayer"] 8165 }, 8166 "dominoSignal": { 8167 "name": "dominoSignal", 8168 "version": "1.4.0", 8169 "sha256": "15ff1p8p5v4gqkv1spnvkx62x5ddbvmd9mxlvkgqmfywzqid2r1h", 8170 "depends": ["ComplexHeatmap", "Matrix", "biomaRt", "circlize", "dplyr", "ggpubr", "igraph", "magrittr", "plyr", "purrr"] 8171 }, 8172 "doppelgangR": { 8173 "name": "doppelgangR", 8174 "version": "1.38.0", 8175 "sha256": "00jn4m8ffp3ql9qhdybjngxjki3g2hpzwdjamld7h6v2gs5dpds7", 8176 "depends": ["Biobase", "BiocParallel", "SummarizedExperiment", "digest", "impute", "mnormt", "sva"] 8177 }, 8178 "doseR": { 8179 "name": "doseR", 8180 "version": "1.26.0", 8181 "sha256": "0v5gnikdjnsyy4iy45wvbhy16z5cbh9wcls460xmxdvxf2c4sb79", 8182 "depends": ["RUnit", "S4Vectors", "SummarizedExperiment", "digest", "edgeR", "lme4", "matrixStats", "mclust"] 8183 }, 8184 "doubletrouble": { 8185 "name": "doubletrouble", 8186 "version": "1.10.0", 8187 "sha256": "129q971qsa4hgvfw2kaf40228ssb4syacj2sb5v59dl41vdlj5ah", 8188 "depends": ["AnnotationDbi", "Biostrings", "GenomicFeatures", "GenomicRanges", "MSA2dist", "ggplot2", "mclust", "rlang", "syntenet"] 8189 }, 8190 "dreamlet": { 8191 "name": "dreamlet", 8192 "version": "1.8.0", 8193 "sha256": "1vz6a353sqgizv41gm2hrc5dzmqlwcmg50p9kscwpzrhpxid7dxn", 8194 "depends": ["BiocGenerics", "BiocParallel", "DelayedArray", "DelayedMatrixStats", "GSEABase", "IRanges", "MASS", "Matrix", "MatrixGenerics", "Rcpp", "Rdpack", "S4Arrays", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "ashr", "beachmat", "broom", "data_table", "dplyr", "edgeR", "ggbeeswarm", "ggplot2", "ggrepel", "gtools", "irlba", "limma", "lme4", "mashr", "metafor", "purrr", "remaCor", "reshape2", "rlang", "scattermore", "sparseMatrixStats", "tidyr", "variancePartition", "zenith"] 8195 }, 8196 "drugTargetInteractions": { 8197 "name": "drugTargetInteractions", 8198 "version": "1.18.0", 8199 "sha256": "056dw485jmlb57w0mwmpww2xrpxkl2lai91rds77vcchvywmpa53", 8200 "depends": ["AnnotationFilter", "BiocFileCache", "RSQLite", "S4Vectors", "UniProt_ws", "biomaRt", "dplyr", "ensembldb", "rappdirs"] 8201 }, 8202 "dupRadar": { 8203 "name": "dupRadar", 8204 "version": "1.40.0", 8205 "sha256": "06xhsss7hqm4n9300ff13zn4w3640i52vf00kdxkvhqzdn2vzwih", 8206 "depends": ["KernSmooth", "Rsubread"] 8207 }, 8208 "dyebias": { 8209 "name": "dyebias", 8210 "version": "1.70.0", 8211 "sha256": "0ylw1wli84p8yxn7sibdg134xkgq52mi7sjpj3sjkym3d70r525i", 8212 "depends": ["Biobase", "marray"] 8213 }, 8214 "easier": { 8215 "name": "easier", 8216 "version": "1.16.0", 8217 "sha256": "0z1znn8c5xkiqvfglqdmip3jh2h0idw8khrnr2hjid1fjxw2y8vf", 8218 "depends": ["BiocParallel", "DESeq2", "ROCR", "coin", "decoupleR", "dorothea", "dplyr", "easierData", "ggplot2", "ggpubr", "ggrepel", "magrittr", "matrixStats", "progeny", "quantiseqr", "reshape2", "rlang", "rstatix", "tibble", "tidyr"] 8219 }, 8220 "easyRNASeq": { 8221 "name": "easyRNASeq", 8222 "version": "2.46.0", 8223 "sha256": "1vbfwgnpbqwcmqvfg4gawk8jazq709gw84wydxywwg9hl3pnxbhf", 8224 "depends": ["Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicAlignments", "GenomicRanges", "IRanges", "LSD", "Rsamtools", "S4Vectors", "Seqinfo", "ShortRead", "SummarizedExperiment", "biomaRt", "edgeR", "genomeIntervals", "rappdirs"] 8225 }, 8226 "easylift": { 8227 "name": "easylift", 8228 "version": "1.8.0", 8229 "sha256": "04fqsf7q6fj1mpz90dj1xd2ndkdvlps72l8yqinhkjpb8wig4kx0", 8230 "depends": ["BiocFileCache", "GenomeInfoDb", "GenomicRanges", "R_utils", "rtracklayer"] 8231 }, 8232 "easyreporting": { 8233 "name": "easyreporting", 8234 "version": "1.22.0", 8235 "sha256": "0a0fl73njp9izd64fn825jjcwic6fb69g03d2dl8c91mkw7m9raf", 8236 "depends": ["rlang", "rmarkdown", "shiny"] 8237 }, 8238 "ecolitk": { 8239 "name": "ecolitk", 8240 "version": "1.82.0", 8241 "sha256": "1zwbrsa3i2arza278475kafd9197lwh3m8yn7rc4w8pgl6qdbjj5", 8242 "depends": ["Biobase"] 8243 }, 8244 "edge": { 8245 "name": "edge", 8246 "version": "2.42.0", 8247 "sha256": "06axdnsa9gi2zxv4a4kraq5nk0hi9p98fsx68nkscsni6v55gdrr", 8248 "depends": ["Biobase", "MASS", "qvalue", "sva"] 8249 }, 8250 "edgeR": { 8251 "name": "edgeR", 8252 "version": "4.8.0", 8253 "sha256": "0r0384f1kxx861diwrwrrqqy0jv0qyc06rfhwl0x1m4lahcb3sk3", 8254 "depends": ["limma", "locfit"] 8255 }, 8256 "eds": { 8257 "name": "eds", 8258 "version": "1.12.0", 8259 "sha256": "0vz9260ahfzp61sw9wm4wpff27lcwmcbk82f2hm3l92qk29dkd0z", 8260 "depends": ["Matrix", "Rcpp"] 8261 }, 8262 "eiR": { 8263 "name": "eiR", 8264 "version": "1.50.0", 8265 "sha256": "1zqd25hnn2nfhc0vb2v5ygwppiv8gndd2282pd0xapv5blqj30jv", 8266 "depends": ["BiocGenerics", "ChemmineR", "DBI", "RCurl", "RUnit", "RcppAnnoy", "digest", "snow", "snowfall"] 8267 }, 8268 "eisaR": { 8269 "name": "eisaR", 8270 "version": "1.22.0", 8271 "sha256": "1c95y084aw3fwz8j2rdkz8zy79k5c9gpg64dry72c587pws7xvq9", 8272 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "edgeR", "limma"] 8273 }, 8274 "enhancerHomologSearch": { 8275 "name": "enhancerHomologSearch", 8276 "version": "1.16.0", 8277 "sha256": "08v24val3dy84fhq1vxxf36w3ya1x0l1sl2yyby4zjhdav7i6nnf", 8278 "depends": ["BSgenome", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "S4Vectors", "Seqinfo", "httr", "jsonlite", "motifmatchr", "pwalign", "rtracklayer"] 8279 }, 8280 "enrichViewNet": { 8281 "name": "enrichViewNet", 8282 "version": "1.8.0", 8283 "sha256": "02xzw4yg9mdc64mgyc25vdyxh5q09c3hpigcyqad80inf6lafy4x", 8284 "depends": ["DOSE", "RCy3", "enrichplot", "gprofiler2", "igraph", "jsonlite", "reshape2", "strex", "stringr"] 8285 }, 8286 "enrichplot": { 8287 "name": "enrichplot", 8288 "version": "1.30.0", 8289 "sha256": "1yh6isyyk58na142zwbaxm9my2vavzyiyafn6kaq2aza7aa2vww7", 8290 "depends": ["DOSE", "GOSemSim", "RColorBrewer", "aplot", "ggfun", "ggnewscale", "ggplot2", "ggrepel", "ggtangle", "ggtree", "igraph", "magrittr", "plyr", "purrr", "reshape2", "rlang", "scatterpie", "yulab_utils"] 8291 }, 8292 "ensembldb": { 8293 "name": "ensembldb", 8294 "version": "2.34.0", 8295 "sha256": "15abvvsm4n26dl5nxrij03xnj3qxai3ckb1fif9x2znvq8127zcd", 8296 "depends": ["AnnotationDbi", "AnnotationFilter", "Biobase", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "ProtGenerics", "RSQLite", "Rsamtools", "S4Vectors", "Seqinfo", "curl", "rtracklayer"] 8297 }, 8298 "epiNEM": { 8299 "name": "epiNEM", 8300 "version": "1.34.0", 8301 "sha256": "0xp69ch3c6r5jn0q8qmwjfmzqxvrwipsk14slxgi6ykxiz6jaqwh", 8302 "depends": ["BoolNet", "BoutrosLab_plotting_general", "RColorBrewer", "e1071", "graph", "gtools", "igraph", "latex2exp", "lattice", "latticeExtra", "minet", "mnem", "pcalg"] 8303 }, 8304 "epialleleR": { 8305 "name": "epialleleR", 8306 "version": "1.18.0", 8307 "sha256": "1d6kkdr9lr01l0agi0gh6674r7rvs5k80kpp36i279v7mz2irs6z", 8308 "depends": ["BH", "BiocGenerics", "GenomicRanges", "Rcpp", "Rhtslib", "data_table"] 8309 }, 8310 "epidecodeR": { 8311 "name": "epidecodeR", 8312 "version": "1.18.0", 8313 "sha256": "1h8za7ijzjmik225zx14yg607adlmvlal7psni9a7n9bpx8jp2pw", 8314 "depends": ["EnvStats", "GenomicRanges", "IRanges", "dplyr", "ggplot2", "ggpubr", "rstatix", "rtracklayer"] 8315 }, 8316 "epigraHMM": { 8317 "name": "epigraHMM", 8318 "version": "1.18.0", 8319 "sha256": "0cicl35l5zcfrxyrg90bd6r1scrizxbfj6vnpizacj6iyf6aj3sg", 8320 "depends": ["GenomicRanges", "GreyListChIP", "IRanges", "MASS", "Matrix", "Rcpp", "RcppArmadillo", "Rhdf5lib", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "bamsignals", "csaw", "data_table", "ggplot2", "ggpubr", "limma", "magrittr", "pheatmap", "rhdf5", "rtracklayer", "scales"] 8321 }, 8322 "epimutacions": { 8323 "name": "epimutacions", 8324 "version": "1.14.0", 8325 "sha256": "1p23md7vyg4lj5x2vdjgq1cfbp0zaxdg6rlmwkwjlbg0ir9mvla2", 8326 "depends": ["AnnotationDbi", "AnnotationHub", "BiocGenerics", "BiocParallel", "ExperimentHub", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Gviz", "Homo_sapiens", "IRanges", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno_ilm10b2_hg19", "IlluminaHumanMethylationEPICmanifest", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg18_knownGene", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "biomaRt", "bumphunter", "ensembldb", "epimutacionsData", "ggplot2", "ggrepel", "gridExtra", "isotree", "matrixStats", "minfi", "purrr", "reshape2", "robustbase", "rtracklayer", "tibble"] 8327 }, 8328 "epiregulon": { 8329 "name": "epiregulon", 8330 "version": "2.0.0", 8331 "sha256": "10k4gi72qsvr2xy9awcjqqfqlz3jkp1ncmnhq6gxa0dsbsdm1lcr", 8332 "depends": ["AnnotationHub", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BSgenome_Mmusculus_UCSC_mm10", "BiocParallel", "ExperimentHub", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "entropy", "lifecycle", "motifmatchr", "scran", "scrapper", "scuttle"] 8333 }, 8334 "epiregulon_extra": { 8335 "name": "epiregulon.extra", 8336 "version": "1.6.0", 8337 "sha256": "0id51n3fpcw3zbzzvyyj30ggw5ab04g8cbw5kh22411a66b1hf9m", 8338 "depends": ["ComplexHeatmap", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "circlize", "clusterProfiler", "ggplot2", "ggraph", "igraph", "patchwork", "reshape2", "scales", "scater", "scran"] 8339 }, 8340 "epistack": { 8341 "name": "epistack", 8342 "version": "1.16.0", 8343 "sha256": "1vdqpdnif38nga5xpnj4d8d1jz0w4rlxnpzbl4d0xm7075zgckhh", 8344 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "plotrix"] 8345 }, 8346 "epistasisGA": { 8347 "name": "epistasisGA", 8348 "version": "1.12.0", 8349 "sha256": "09svmywzzip89jdz6wc7c4sqlilyvkwr4sqc41dr6d615z88z755", 8350 "depends": ["BH", "BiocParallel", "Rcpp", "RcppArmadillo", "batchtools", "bigmemory", "data_table", "ggplot2", "igraph", "matrixStats", "qgraph", "survival"] 8351 }, 8352 "epivizr": { 8353 "name": "epivizr", 8354 "version": "2.40.0", 8355 "sha256": "1yhn33p12497p2zzf6sar93gb9par2d4hsiq63kpjky6c8g3xw95", 8356 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "bumphunter", "epivizrData", "epivizrServer"] 8357 }, 8358 "epivizrChart": { 8359 "name": "epivizrChart", 8360 "version": "1.32.0", 8361 "sha256": "17sc1wd55vjakb62341w8xgpvy2dz16zwy5ryyzdkvlwgp002f9x", 8362 "depends": ["BiocGenerics", "epivizrData", "epivizrServer", "htmltools", "rjson"] 8363 }, 8364 "epivizrData": { 8365 "name": "epivizrData", 8366 "version": "1.38.0", 8367 "sha256": "19nkckx5a54zl3r3ck7nfnqzsjw0r6dxindd0gfx8jm9b9y9yxs3", 8368 "depends": ["Biobase", "GenomicFeatures", "GenomicRanges", "IRanges", "OrganismDbi", "S4Vectors", "Seqinfo", "SummarizedExperiment", "ensembldb", "epivizrServer"] 8369 }, 8370 "epivizrServer": { 8371 "name": "epivizrServer", 8372 "version": "1.38.0", 8373 "sha256": "19lvghdnq6p2lr280ml0wvmh6q1071x2l1pacf2p354va0idkxkm", 8374 "depends": ["R6", "httpuv", "mime", "rjson"] 8375 }, 8376 "epivizrStandalone": { 8377 "name": "epivizrStandalone", 8378 "version": "1.38.0", 8379 "sha256": "0l253z1fvxll449p5nvp0qy43xkzmk6mggyacw3fbkfndlakpv5a", 8380 "depends": ["BiocGenerics", "GenomicFeatures", "S4Vectors", "Seqinfo", "epivizr", "epivizrServer", "git2r"] 8381 }, 8382 "erccdashboard": { 8383 "name": "erccdashboard", 8384 "version": "1.44.0", 8385 "sha256": "0af77ir60aqlg5589hkkcr5hapl9nymgxc1m3j2cb5hg23nsw3j4", 8386 "depends": ["MASS", "ROCR", "edgeR", "ggplot2", "gplots", "gridExtra", "gtools", "knitr", "limma", "locfit", "plyr", "qvalue", "reshape2", "scales", "stringr"] 8387 }, 8388 "esATAC": { 8389 "name": "esATAC", 8390 "version": "1.32.0", 8391 "sha256": "0gvw67vdw2bcjn7g4077397vsf3lgfdayfxym5miz3gd0bdd8gln", 8392 "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "BiocManager", "Biostrings", "ChIPseeker", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "JASPAR2018", "R_utils", "Rbowtie2", "Rcpp", "Rsamtools", "S4Vectors", "Seqinfo", "ShortRead", "TFBSTools", "VennDiagram", "clusterProfiler", "corrplot", "digest", "ggplot2", "igraph", "knitr", "magrittr", "motifmatchr", "pipeFrame", "rJava", "rmarkdown", "rtracklayer"] 8393 }, 8394 "escape": { 8395 "name": "escape", 8396 "version": "2.5.5", 8397 "sha256": "0i8d7qsc0mb6zlcwahi9f4gmx71as49wj09l82hkyvf0g50b30wc", 8398 "depends": ["Matrix", "MatrixGenerics", "SummarizedExperiment", "ggdist", "ggplot2"] 8399 }, 8400 "escheR": { 8401 "name": "escheR", 8402 "version": "1.10.0", 8403 "sha256": "0blmmcn2vys0pkkyfhbwy1lpywbcb9m4yp2xz4njgq3iml5bb98x", 8404 "depends": ["SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "rlang"] 8405 }, 8406 "esetVis": { 8407 "name": "esetVis", 8408 "version": "1.36.0", 8409 "sha256": "1crl2f2wxb98k1xjmbcbl143wpy6nv2blmyl78iix154pjcb7rkv", 8410 "depends": ["Biobase", "MASS", "MLP", "Rtsne", "hexbin", "mpm"] 8411 }, 8412 "eudysbiome": { 8413 "name": "eudysbiome", 8414 "version": "1.40.0", 8415 "sha256": "1zxh2gpbhl2sbpv0yrhay3rxkcv5mcgmdmc99ixmj9lfrw1zl4nv", 8416 "depends": ["Biostrings", "R_utils", "Rsamtools", "plyr"] 8417 }, 8418 "evaluomeR": { 8419 "name": "evaluomeR", 8420 "version": "1.26.0", 8421 "sha256": "1disy9mbq8090bsl429lz0b30vb7k2ss3qyrcig8i3ldsyr9gw25", 8422 "depends": ["MASS", "MultiAssayExperiment", "RSKC", "Rdpack", "SummarizedExperiment", "class", "cluster", "corrplot", "dendextend", "dplyr", "flexmix", "fpc", "ggdendro", "ggplot2", "kableExtra", "matrixStats", "mclust", "plotrix", "prabclus", "randomForest", "reshape2", "sparcl"] 8423 }, 8424 "extraChIPs": { 8425 "name": "extraChIPs", 8426 "version": "1.14.0", 8427 "sha256": "08lk9lqiincl5g4r9lmra3557jn6vklmsc6c2iw142j9xr3y8d0v", 8428 "depends": ["BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "csaw", "dplyr", "edgeR", "forcats", "ggplot2", "ggrepel", "ggside", "glue", "matrixStats", "patchwork", "rlang", "rtracklayer", "scales", "stringr", "tibble", "tidyr", "tidyselect", "vctrs"] 8429 }, 8430 "fCCAC": { 8431 "name": "fCCAC", 8432 "version": "1.36.0", 8433 "sha256": "00mcnlfawsvya1rclivkkig5nfwlb47kc44b2xvfk2njkild8fbd", 8434 "depends": ["ComplexHeatmap", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "fda", "genomation", "ggplot2"] 8435 }, 8436 "fCI": { 8437 "name": "fCI", 8438 "version": "1.40.0", 8439 "sha256": "1icdmwbl27c7i2hrkhqj201fnbzj5g6ybhmv2dd5lfhpx3gww6lr", 8440 "depends": ["FNN", "VennDiagram", "gtools", "psych", "rgl", "zoo"] 8441 }, 8442 "fabia": { 8443 "name": "fabia", 8444 "version": "2.56.0", 8445 "sha256": "1419icrgj7hxi713f4l2l6sqfxh9g1c49g4ls879bvfssxndsxds", 8446 "depends": ["Biobase"] 8447 }, 8448 "factDesign": { 8449 "name": "factDesign", 8450 "version": "1.86.0", 8451 "sha256": "174r4prhhp2fbl9kaxp28p36srj65pp72lxqwicsr25vwkp4vfvs", 8452 "depends": ["Biobase"] 8453 }, 8454 "faers": { 8455 "name": "faers", 8456 "version": "1.6.0", 8457 "sha256": "1w6b5h3ww33nydfwa2hbmxag9am7wd39gmsm5155bl83qrdyxxfa", 8458 "depends": ["BiocParallel", "MCMCpack", "brio", "cli", "curl", "data_table", "httr2", "openEBGM", "rlang", "rvest", "vroom", "xml2"] 8459 }, 8460 "fastLiquidAssociation": { 8461 "name": "fastLiquidAssociation", 8462 "version": "1.46.0", 8463 "sha256": "0qvacr9486r6sdw3f6rxrs7rhhk0aigsxjqqib771vi69q480bf4", 8464 "depends": ["Hmisc", "LiquidAssociation", "WGCNA", "doParallel", "impute", "preprocessCore"] 8465 }, 8466 "fastreeR": { 8467 "name": "fastreeR", 8468 "version": "2.0.0", 8469 "sha256": "02pw9gsakadzb7p1k1fk6ynqyqlflxilw7mvgjn94z11lzjvxfx4", 8470 "depends": ["R_utils", "ape", "data_table", "dynamicTreeCut", "rJava", "stringr"] 8471 }, 8472 "fastseg": { 8473 "name": "fastseg", 8474 "version": "1.56.0", 8475 "sha256": "0q007hg6afi4h05gkw1hm7aqi0g9lzqxnq6yljkl14lvw0ihjb3h", 8476 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors"] 8477 }, 8478 "fcScan": { 8479 "name": "fcScan", 8480 "version": "1.24.0", 8481 "sha256": "0w4g65qcaxy8x30r1f638dm69kslxab2gy761ggvb8if5r7631sb", 8482 "depends": ["GenomicRanges", "IRanges", "SummarizedExperiment", "VariantAnnotation", "doParallel", "foreach", "plyr", "rtracklayer"] 8483 }, 8484 "fdrame": { 8485 "name": "fdrame", 8486 "version": "1.82.0", 8487 "sha256": "1526yh6rbimf0lnpmbi2dhamfrcfahfb85q23h3i6x0pcrp3nw2f", 8488 "depends": [] 8489 }, 8490 "fedup": { 8491 "name": "fedup", 8492 "version": "1.18.0", 8493 "sha256": "0lv648vh8kp14b1alnp5p5x3kykj5sb19rp3vs7nf0fqr1yid3xn", 8494 "depends": ["RColorBrewer", "RCy3", "data_table", "dplyr", "forcats", "ggplot2", "ggthemes", "openxlsx", "tibble"] 8495 }, 8496 "fenr": { 8497 "name": "fenr", 8498 "version": "1.8.0", 8499 "sha256": "0lpfach366p3z9y0z0r6xgv5yk02dr0782caxhjsix7jid1rf48v", 8500 "depends": ["BiocFileCache", "assertthat", "dplyr", "ggplot2", "httr2", "progress", "purrr", "readr", "rlang", "rvest", "shiny", "stringr", "tibble", "tidyr", "tidyselect"] 8501 }, 8502 "ffpe": { 8503 "name": "ffpe", 8504 "version": "1.54.0", 8505 "sha256": "18k4i9hy7c1hrpm8cqi1npx4dq9fand6lrdk92mbr7lcgl3w25lh", 8506 "depends": ["Biobase", "BiocGenerics", "TTR", "affy", "lumi", "methylumi", "sfsmisc"] 8507 }, 8508 "fgga": { 8509 "name": "fgga", 8510 "version": "1.18.0", 8511 "sha256": "1hz72m434axgiikh8bfk5jb16aq920y8wqimphpd27v8iq452fv1", 8512 "depends": ["BiocFileCache", "RBGL", "curl", "e1071", "gRbase", "graph", "igraph", "jsonlite"] 8513 }, 8514 "fgsea": { 8515 "name": "fgsea", 8516 "version": "1.36.0", 8517 "sha256": "040z8k28zg9rlvlrywp1ah39pcll74jdmfzhy2r7rijmmvw8ypip", 8518 "depends": ["BH", "BiocParallel", "Matrix", "Rcpp", "cowplot", "data_table", "fastmatch", "ggplot2", "scales"] 8519 }, 8520 "findIPs": { 8521 "name": "findIPs", 8522 "version": "1.6.0", 8523 "sha256": "1fw8zjnn9ayijqjjmjx7w7jpwrsfcnlinznqvjd4qsi0bz8zir3b", 8524 "depends": ["Biobase", "BiocParallel", "SummarizedExperiment", "survival"] 8525 }, 8526 "fishpond": { 8527 "name": "fishpond", 8528 "version": "2.16.0", 8529 "sha256": "0bqbsciq0yxldc8zdjj829n11pn2r4qrc4wsnarm2dp49dy4ipp3", 8530 "depends": ["GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "abind", "gtools", "jsonlite", "matrixStats", "qvalue", "svMisc"] 8531 }, 8532 "flagme": { 8533 "name": "flagme", 8534 "version": "1.66.0", 8535 "sha256": "0zyjvwd4xgdy0brfb8xyq1h4il8gx65s2smk7395qh87fqbkd05k", 8536 "depends": ["CAMERA", "MASS", "SparseM", "gcspikelite", "gplots", "xcms"] 8537 }, 8538 "flowAI": { 8539 "name": "flowAI", 8540 "version": "1.40.0", 8541 "sha256": "095410xm3zmbbp5sfwp581mhnndcsq4g325f4i0gka1ll5hqnwqm", 8542 "depends": ["RColorBrewer", "changepoint", "flowCore", "ggplot2", "knitr", "plyr", "reshape2", "rmarkdown", "scales"] 8543 }, 8544 "flowBeads": { 8545 "name": "flowBeads", 8546 "version": "1.48.0", 8547 "sha256": "1gnxbz9lpiigaa5yk83k8vz15jd2ci86ya973m92ijdij3pkrc7h", 8548 "depends": ["Biobase", "flowCore", "knitr", "rrcov", "xtable"] 8549 }, 8550 "flowBin": { 8551 "name": "flowBin", 8552 "version": "1.46.0", 8553 "sha256": "1r9hddrwq9s5i83j2scppg7cqbn9fr0ymyrh7wwbs22h83qwbcsj", 8554 "depends": ["BiocGenerics", "class", "flowCore", "flowFP", "limma", "snow"] 8555 }, 8556 "flowCHIC": { 8557 "name": "flowCHIC", 8558 "version": "1.44.0", 8559 "sha256": "0qxy6s6l6m0whw33sf105bh683f56fmhdnf6wnq7ig00llm8c902", 8560 "depends": ["EBImage", "flowCore", "ggplot2", "hexbin", "vegan"] 8561 }, 8562 "flowClean": { 8563 "name": "flowClean", 8564 "version": "1.48.0", 8565 "sha256": "1njbcr86x13pbp43aiacjpqxbfkiqdzdzddqrd8d9fkmsknfbbfh", 8566 "depends": ["bit", "changepoint", "flowCore", "sfsmisc"] 8567 }, 8568 "flowClust": { 8569 "name": "flowClust", 8570 "version": "3.48.0", 8571 "sha256": "1ncx63ynqxaldc8mb68k8jwq116myml6ccgh9j7n5dcvhfcqgqf1", 8572 "depends": ["Biobase", "BiocGenerics", "flowCore", "graph"] 8573 }, 8574 "flowCore": { 8575 "name": "flowCore", 8576 "version": "2.22.0", 8577 "sha256": "0rmlff8d36z8d59s9w4va0csdklz6vkl8k0ywyg6rgmg5k327jqd", 8578 "depends": ["BH", "Biobase", "BiocGenerics", "RProtoBufLib", "Rcpp", "S4Vectors", "cpp11", "cytolib", "matrixStats"] 8579 }, 8580 "flowCut": { 8581 "name": "flowCut", 8582 "version": "1.20.0", 8583 "sha256": "1zism6y5gcqklncblf9ksbsnv2ic06djr4aq9h01ixjmmh1f4w72", 8584 "depends": ["Cairo", "e1071", "flowCore", "flowDensity"] 8585 }, 8586 "flowCyBar": { 8587 "name": "flowCyBar", 8588 "version": "1.46.0", 8589 "sha256": "1ckzmjnjhjdw32mli8pyqgkmq6kk64vdm99qy165q32p39gfp3wl", 8590 "depends": ["gplots", "vegan"] 8591 }, 8592 "flowDensity": { 8593 "name": "flowDensity", 8594 "version": "1.44.0", 8595 "sha256": "0rxjwx9pynpz0ylf8znd4h61qazl91p1s2435dsl654ik7wpqw8c", 8596 "depends": ["car", "flowCore", "flowViz", "gplots", "polyclip"] 8597 }, 8598 "flowFP": { 8599 "name": "flowFP", 8600 "version": "1.68.0", 8601 "sha256": "1ngn0b3k28fksl6xx65634i138j87mn0s6myiw40blc2c485i9xz", 8602 "depends": ["Biobase", "BiocGenerics", "flowCore", "flowViz"] 8603 }, 8604 "flowGate": { 8605 "name": "flowGate", 8606 "version": "1.10.0", 8607 "sha256": "0ddavbhgw62w2alj972n0q4l61ilz1iqnrc1mwdwaps0208b5l5d", 8608 "depends": ["BiocManager", "dplyr", "flowCore", "flowWorkspace", "ggcyto", "ggplot2", "purrr", "rlang", "shiny", "tibble"] 8609 }, 8610 "flowGraph": { 8611 "name": "flowGraph", 8612 "version": "1.18.0", 8613 "sha256": "0dy2jygbm3dzcsh33abah8cnz9srxw2234qfyl0jrzpwnfs0c8vd", 8614 "depends": ["Matrix", "Rdpack", "data_table", "effsize", "furrr", "future", "ggiraph", "ggplot2", "ggrepel", "gridExtra", "htmlwidgets", "igraph", "matrixStats", "purrr", "stringi", "stringr", "visNetwork"] 8615 }, 8616 "flowMatch": { 8617 "name": "flowMatch", 8618 "version": "1.46.0", 8619 "sha256": "0p8v6bxbc3mnwjf8lf6d5zqlddlcacwsayla2wbb0535dfvkfmjp", 8620 "depends": ["Biobase", "Rcpp", "flowCore"] 8621 }, 8622 "flowMeans": { 8623 "name": "flowMeans", 8624 "version": "1.70.0", 8625 "sha256": "0q2pnfadn8f4hhn2qd7yqrdl9hkjmcqizm5wjjybrhxq1g8sb15d", 8626 "depends": ["Biobase", "feature", "flowCore", "rrcov"] 8627 }, 8628 "flowMerge": { 8629 "name": "flowMerge", 8630 "version": "2.58.0", 8631 "sha256": "0j0m6r06gpxbjlr1x3cjx1iyp78b61kmdxs0d9fby7mjjj67k8jc", 8632 "depends": ["Rgraphviz", "feature", "flowClust", "flowCore", "foreach", "graph", "rrcov", "snow"] 8633 }, 8634 "flowPeaks": { 8635 "name": "flowPeaks", 8636 "version": "1.56.0", 8637 "sha256": "1znvp3in8l6rcmmfbir2b94wgbmdf9bwisp21c5cfkxq5yckwdvx", 8638 "depends": [] 8639 }, 8640 "flowPloidy": { 8641 "name": "flowPloidy", 8642 "version": "1.36.0", 8643 "sha256": "0z8rrrw8c9pxp14dcdlb2g515krimv9hbmaivifrpswxhpwq6qln", 8644 "depends": ["caTools", "car", "flowCore", "knitr", "minpack_lm", "rmarkdown", "shiny"] 8645 }, 8646 "flowPlots": { 8647 "name": "flowPlots", 8648 "version": "1.58.0", 8649 "sha256": "1hihd7jsfnhil3zisb1yhnc5p8qwxw681d2vj1zpg28lklvx702p", 8650 "depends": [] 8651 }, 8652 "flowSpecs": { 8653 "name": "flowSpecs", 8654 "version": "1.24.0", 8655 "sha256": "01an7rpmhwlvxh5y4silc4508yqp404g4fxsm2d9gjp3xpgwj2qn", 8656 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "flowCore", "ggplot2", "reshape2", "zoo"] 8657 }, 8658 "flowStats": { 8659 "name": "flowStats", 8660 "version": "4.22.0", 8661 "sha256": "0hf1y1bgvvnr3g8zj246pzyrl5p5811m509dvwd1jmzqri129fcl", 8662 "depends": ["Biobase", "BiocGenerics", "KernSmooth", "MASS", "RColorBrewer", "clue", "cluster", "corpcor", "fda", "flowCore", "flowViz", "flowWorkspace", "ks", "lattice", "mnormt", "ncdfFlow", "rrcov"] 8663 }, 8664 "flowTime": { 8665 "name": "flowTime", 8666 "version": "1.34.0", 8667 "sha256": "15djxvxcffncxywwviwwgw2g09j1w4y5a293b6cs3paqlp6w05ba", 8668 "depends": ["dplyr", "flowCore", "magrittr", "plyr", "rlang", "tibble"] 8669 }, 8670 "flowTrans": { 8671 "name": "flowTrans", 8672 "version": "1.62.0", 8673 "sha256": "16h776hi33axcqr9v7lcvzmrzh273gyg8gc1ybyi8j12ry5wlbrs", 8674 "depends": ["flowClust", "flowCore", "flowViz"] 8675 }, 8676 "flowVS": { 8677 "name": "flowVS", 8678 "version": "1.42.0", 8679 "sha256": "0j7q9i3qy15xwncj7mhzmvivl45h7pykpk8ps3zlc5hmwv3ri9qm", 8680 "depends": ["flowCore", "flowStats", "flowViz"] 8681 }, 8682 "flowViz": { 8683 "name": "flowViz", 8684 "version": "1.74.0", 8685 "sha256": "1615f5r2y51dazynjsihxp4q56zgn70wfd5fjcvr0pw3l7wbh77n", 8686 "depends": ["Biobase", "IDPmisc", "KernSmooth", "MASS", "RColorBrewer", "flowCore", "hexbin", "lattice", "latticeExtra"] 8687 }, 8688 "flowWorkspace": { 8689 "name": "flowWorkspace", 8690 "version": "4.22.0", 8691 "sha256": "1hy44nyhgk8z85lis8nz1djsma4wyanixibs7qds0xgimk5r9qqq", 8692 "depends": ["BH", "Biobase", "BiocGenerics", "DelayedArray", "RBGL", "RProtoBufLib", "Rgraphviz", "Rhdf5lib", "S4Vectors", "XML", "cpp11", "cytolib", "data_table", "dplyr", "flowCore", "ggplot2", "graph", "matrixStats", "ncdfFlow", "scales"] 8693 }, 8694 "flowcatchR": { 8695 "name": "flowcatchR", 8696 "version": "1.44.0", 8697 "sha256": "17nww1smm4vvfqfgjsdabcvix4hd836601y5cq0wial6y3ixhhmy", 8698 "depends": ["BiocParallel", "EBImage", "abind", "colorRamps", "plotly", "shiny"] 8699 }, 8700 "fmcsR": { 8701 "name": "fmcsR", 8702 "version": "1.52.0", 8703 "sha256": "1x4hczppvdgsmdn57fmfkr9gcfj952jslha5fshs6pbyyq2xqjik", 8704 "depends": ["BiocGenerics", "ChemmineR", "RUnit"] 8705 }, 8706 "fmrs": { 8707 "name": "fmrs", 8708 "version": "1.20.0", 8709 "sha256": "1ai903fi74kl10d6bamaaf75zclyvff589chad2z9xymf4ixybsc", 8710 "depends": ["survival"] 8711 }, 8712 "fobitools": { 8713 "name": "fobitools", 8714 "version": "1.18.0", 8715 "sha256": "0bczh98lppj4kr0rbd1jsxc3syg3113f38h89y258b21m1ivp7my", 8716 "depends": ["RecordLinkage", "clisymbols", "crayon", "dplyr", "fgsea", "ggplot2", "ggraph", "magrittr", "ontologyIndex", "purrr", "stringr", "textclean", "tictoc", "tidygraph", "tidyr", "vroom"] 8717 }, 8718 "frenchFISH": { 8719 "name": "frenchFISH", 8720 "version": "1.22.0", 8721 "sha256": "1fxd9p742j9svl0j86357iiy0h9slka69dgll58vmlrs4xzyq3p0", 8722 "depends": ["MCMCpack", "NHPoisson"] 8723 }, 8724 "frma": { 8725 "name": "frma", 8726 "version": "1.62.0", 8727 "sha256": "0kiwvcivw27m394ls3qx7cl7lazbpa4kg4lg3hlg12jqzpb3z6dx", 8728 "depends": ["Biobase", "BiocGenerics", "DBI", "MASS", "affy", "oligo", "oligoClasses", "preprocessCore"] 8729 }, 8730 "frmaTools": { 8731 "name": "frmaTools", 8732 "version": "1.62.0", 8733 "sha256": "0w3igjhqd2whmcvvwdjsgws1q4gb74d9gn7sgkb0zjc41rrh416c", 8734 "depends": ["Biobase", "DBI", "affy", "preprocessCore"] 8735 }, 8736 "funOmics": { 8737 "name": "funOmics", 8738 "version": "1.4.0", 8739 "sha256": "1sqalmryyvgd68prhjvp9xmnx5v8sjirxpr86vv070ag75j4hs91", 8740 "depends": ["AnnotationDbi", "KEGGREST", "NMF", "dplyr", "org_Hs_eg_db", "pathifier", "stringr"] 8741 }, 8742 "funtooNorm": { 8743 "name": "funtooNorm", 8744 "version": "1.34.0", 8745 "sha256": "1ka05p1cmv2cmlawir25c12hwb51bnnd8s327qqb3xyigkb32nb8", 8746 "depends": ["GenomeInfoDb", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "matrixStats", "minfi", "pls"] 8747 }, 8748 "gCrisprTools": { 8749 "name": "gCrisprTools", 8750 "version": "2.16.0", 8751 "sha256": "1i7gz0yalkdjgkx7ma3yrvyj5rj19s2cjy9wc2z6nkcbhqw7i8m7", 8752 "depends": ["Biobase", "ComplexHeatmap", "RobustRankAggreg", "SummarizedExperiment", "ggplot2", "limma", "rmarkdown"] 8753 }, 8754 "gDNAx": { 8755 "name": "gDNAx", 8756 "version": "1.8.0", 8757 "sha256": "0nzqf4rnvn42br0awr8qwmp0w4cjnp6rwv414rz51pgan59vgcg9", 8758 "depends": ["AnnotationDbi", "AnnotationHub", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "bitops", "cli", "matrixStats", "plotrix"] 8759 }, 8760 "gDR": { 8761 "name": "gDR", 8762 "version": "1.8.0", 8763 "sha256": "0h7pjvrjl2l6h51vnws4mkxgfl9q3xpn9gakv5imqfliw22q23mp", 8764 "depends": ["gDRcore", "gDRimport", "gDRutils"] 8765 }, 8766 "gDRcore": { 8767 "name": "gDRcore", 8768 "version": "1.8.0", 8769 "sha256": "1h0najhngsqcyn431wixj82j6j2j9mx5qj7whssm0db48dj1y71k", 8770 "depends": ["BiocParallel", "BumpyMatrix", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "checkmate", "data_table", "futile_logger", "gDRutils", "purrr", "stringr"] 8771 }, 8772 "gDRimport": { 8773 "name": "gDRimport", 8774 "version": "1.8.0", 8775 "sha256": "1lxl7m5lvza1jwcbbfh71jwjn1s17ys06skwxmz6k98nbdgx98nh", 8776 "depends": ["BumpyMatrix", "CoreGx", "MultiAssayExperiment", "PharmacoGx", "S4Vectors", "SummarizedExperiment", "XML", "assertthat", "checkmate", "data_table", "futile_logger", "gDRutils", "magrittr", "openxlsx", "readxl", "rio", "stringi", "tibble", "yaml"] 8777 }, 8778 "gDRstyle": { 8779 "name": "gDRstyle", 8780 "version": "1.8.0", 8781 "sha256": "1qip0l8qg972yrb4mhzp74ils8d2iw9j5df3kfi9rsblzbqz7093", 8782 "depends": ["BiocCheck", "BiocManager", "BiocStyle", "checkmate", "desc", "git2r", "lintr", "pkgbuild", "rcmdcheck", "remotes", "rjson", "withr", "yaml"] 8783 }, 8784 "gDRutils": { 8785 "name": "gDRutils", 8786 "version": "1.8.0", 8787 "sha256": "0fmga9d395srdlsmw4ivpm5x99snyg6pwd9qp80xfjf4y62k1p47", 8788 "depends": ["BiocParallel", "BumpyMatrix", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "checkmate", "data_table", "digest", "drc", "jsonlite", "jsonvalidate", "qs", "stringr"] 8789 }, 8790 "gVenn": { 8791 "name": "gVenn", 8792 "version": "1.0.0", 8793 "sha256": "146596jgp3g7xiismdll8l0sfhyragn3ggpln2jmjqmk868k2hzc", 8794 "depends": ["ComplexHeatmap", "GenomicRanges", "IRanges", "eulerr", "lubridate", "rtracklayer", "stringr", "writexl"] 8795 }, 8796 "gaga": { 8797 "name": "gaga", 8798 "version": "2.56.0", 8799 "sha256": "0zia3kqnxfcvkc8jijzgmhkm3nk43nvd5z84aanbzzqrmnxlws4j", 8800 "depends": ["Biobase", "EBarrays", "coda", "mgcv"] 8801 }, 8802 "gage": { 8803 "name": "gage", 8804 "version": "2.60.0", 8805 "sha256": "0qza3nm3fmm6g8jsymiv7k8pqygxb1c4gys5gf65nj3gbwrnscba", 8806 "depends": ["AnnotationDbi", "GO_db", "KEGGREST", "graph"] 8807 }, 8808 "garfield": { 8809 "name": "garfield", 8810 "version": "1.38.0", 8811 "sha256": "1xw5ylns5jfjlbz0m3kdp71067p6rxlg8zxmx5xvnr1igqmz8mk0", 8812 "depends": [] 8813 }, 8814 "gatom": { 8815 "name": "gatom", 8816 "version": "1.8.0", 8817 "sha256": "1sps2fmi2dwxxrnf0l7rf58ng8mqhfx2lr44vrhhgmbvc9n7gsnr", 8818 "depends": ["BioNet", "GGally", "XML", "data_table", "ggplot2", "htmltools", "htmlwidgets", "igraph", "intergraph", "mwcsr", "network", "plyr", "pryr", "shinyCyJS", "sna"] 8819 }, 8820 "gcapc": { 8821 "name": "gcapc", 8822 "version": "1.34.0", 8823 "sha256": "157jslmk9big03fag3687v9gzi8r6fmvcbx819sv344qjw6iid95", 8824 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "Rsamtools", "S4Vectors", "Seqinfo", "matrixStats"] 8825 }, 8826 "gcatest": { 8827 "name": "gcatest", 8828 "version": "2.10.0", 8829 "sha256": "0ay9ji48x3ypz7x8x7qhrp6r762p021c1hmc0j12sgs1f3wkwbh9", 8830 "depends": ["lfa"] 8831 }, 8832 "gcrma": { 8833 "name": "gcrma", 8834 "version": "2.82.0", 8835 "sha256": "1q37xcka0lxacslrbka36kic0fb3w7qsy1rl78spbzdykzxbgnc1", 8836 "depends": ["Biobase", "BiocManager", "Biostrings", "XVector", "affy", "affyio"] 8837 }, 8838 "gdsfmt": { 8839 "name": "gdsfmt", 8840 "version": "1.46.0", 8841 "sha256": "0kc4s5c82qbkrbfqg1n46302ab3in7z106jgsdvbj3k3ms2d6y4v", 8842 "depends": [] 8843 }, 8844 "geNetClassifier": { 8845 "name": "geNetClassifier", 8846 "version": "1.50.0", 8847 "sha256": "1hsm0zbzw5syz9f0jrwxlczac11xc8as9w9vlhibwmc7hm8aasqx", 8848 "depends": ["Biobase", "EBarrays", "e1071", "minet"] 8849 }, 8850 "gemini": { 8851 "name": "gemini", 8852 "version": "1.24.0", 8853 "sha256": "0kw4hkgv7w31wmjjgwwq5d3d52mfb8v37yqvicbkp1ah3i2w9wl9", 8854 "depends": ["dplyr", "ggplot2", "magrittr", "mixtools", "pbmcapply", "scales"] 8855 }, 8856 "gemma_R": { 8857 "name": "gemma.R", 8858 "version": "3.6.0", 8859 "sha256": "1p23x7jnsi4ja8f45pf2vqlyx26730nhfhlxrc3kq0qkhx10xyl1", 8860 "depends": ["Biobase", "R_utils", "S4Vectors", "SummarizedExperiment", "assertthat", "base64enc", "bit64", "data_table", "digest", "glue", "httr", "jsonlite", "kableExtra", "lubridate", "magrittr", "memoise", "rappdirs", "rlang", "stringr", "tibble", "tidyr"] 8861 }, 8862 "genArise": { 8863 "name": "genArise", 8864 "version": "1.86.0", 8865 "sha256": "1kv4f2d0zlm5nikz3wqs66g648ag1m2fx64lq29q37hnpaz25xib", 8866 "depends": ["locfit", "tkrplot", "xtable"] 8867 }, 8868 "geneAttribution": { 8869 "name": "geneAttribution", 8870 "version": "1.36.0", 8871 "sha256": "14ba7smlaij0h0lmp3z63mzhbni9p26anl8psdl5aaqvlvkzaqkr", 8872 "depends": ["BiocGenerics", "GenomicFeatures", "GenomicRanges", "IRanges", "Seqinfo", "org_Hs_eg_db", "rtracklayer"] 8873 }, 8874 "geneClassifiers": { 8875 "name": "geneClassifiers", 8876 "version": "1.34.0", 8877 "sha256": "1avhd24hcfh0a8g0h5171rbxrqnf8bq3frdspqnkls3f7vzqx2b2", 8878 "depends": ["Biobase", "BiocGenerics"] 8879 }, 8880 "geneRecommender": { 8881 "name": "geneRecommender", 8882 "version": "1.82.0", 8883 "sha256": "037m4fhflfqa4jpms9200qb5l9j780b3glwfr5vff37hy1rr7wag", 8884 "depends": ["Biobase"] 8885 }, 8886 "geneRxCluster": { 8887 "name": "geneRxCluster", 8888 "version": "1.46.0", 8889 "sha256": "1ay2n9p707qkiwvqblm39yys8mnfq7zbps2j1yx8vcq5l8h42hsl", 8890 "depends": ["GenomicRanges", "IRanges"] 8891 }, 8892 "geneXtendeR": { 8893 "name": "geneXtendeR", 8894 "version": "1.36.0", 8895 "sha256": "1cirzfrxwrqqakpwizih0ixvxnkvj7vmphr5nwrvmhpfbavs3dkf", 8896 "depends": ["AnnotationDbi", "BiocStyle", "GO_db", "RColorBrewer", "SnowballC", "data_table", "dplyr", "networkD3", "org_Rn_eg_db", "rtracklayer", "tm", "wordcloud"] 8897 }, 8898 "genefilter": { 8899 "name": "genefilter", 8900 "version": "1.92.0", 8901 "sha256": "1snc3xkw1x2d6cbxsprpbnhh9ywcb0mf56qgm2hnd1qyy1ldaylc", 8902 "depends": ["AnnotationDbi", "Biobase", "MatrixGenerics", "annotate", "survival"] 8903 }, 8904 "genefu": { 8905 "name": "genefu", 8906 "version": "2.42.0", 8907 "sha256": "11264hwfp1wkbnq2y7i4n8xh2hamq8qc92jb6shyl84fc6m2c21z", 8908 "depends": ["AIMS", "amap", "biomaRt", "iC10", "iC10TrainingData", "impute", "limma", "mclust", "survcomp"] 8909 }, 8910 "geneplast": { 8911 "name": "geneplast", 8912 "version": "1.36.0", 8913 "sha256": "1p3rav9c8fzq1mwi93w4rcg9y92m3rxg98qqn1khg7m7dq1vqkpr", 8914 "depends": ["ape", "data_table", "igraph", "snow"] 8915 }, 8916 "geneplotter": { 8917 "name": "geneplotter", 8918 "version": "1.88.0", 8919 "sha256": "1b2iq04rxzq28bihr9abhk66ynnjizkgkdls66r2g3r3kdm66xzm", 8920 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "RColorBrewer", "annotate", "lattice"] 8921 }, 8922 "genomation": { 8923 "name": "genomation", 8924 "version": "1.42.0", 8925 "sha256": "1v0zq82cg4vixmsa4plcjf0zp1zvw1m4g54micazkzjkyxsfcfvh", 8926 "depends": ["BSgenome", "Biostrings", "GenomicAlignments", "GenomicRanges", "IRanges", "Rcpp", "Rsamtools", "S4Vectors", "Seqinfo", "data_table", "ggplot2", "gridBase", "impute", "matrixStats", "plotrix", "plyr", "readr", "reshape2", "rtracklayer", "seqPattern"] 8927 }, 8928 "genomeIntervals": { 8929 "name": "genomeIntervals", 8930 "version": "1.66.0", 8931 "sha256": "0igfivmkfbd299gbrwabbfs8n1m79xy1irgsnsj89bw7xxmasxxa", 8932 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "intervals"] 8933 }, 8934 "genomes": { 8935 "name": "genomes", 8936 "version": "3.40.0", 8937 "sha256": "1ygp7gcn791hkny17y01ycg193zf6aibab9493vs8w15k9zjv5h9", 8938 "depends": ["curl", "readr"] 8939 }, 8940 "genomicInstability": { 8941 "name": "genomicInstability", 8942 "version": "1.16.0", 8943 "sha256": "0pbzh2a0m94bqshmkw5fgd9scsn82k3vfmk67hlpkfi36kj18ws0", 8944 "depends": ["SummarizedExperiment", "checkmate", "mixtools"] 8945 }, 8946 "geomeTriD": { 8947 "name": "geomeTriD", 8948 "version": "1.4.0", 8949 "sha256": "0cpvbmdv7wbsd284kqxh621vm60b98slj52cj6nsrli77rz5nm06", 8950 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "InteractionSet", "MASS", "Matrix", "RANN", "S4Vectors", "Seqinfo", "aricode", "clue", "cluster", "dbscan", "future_apply", "htmlwidgets", "igraph", "plotrix", "progressr", "rgl", "rjson", "scales", "trackViewer"] 8951 }, 8952 "gep2pep": { 8953 "name": "gep2pep", 8954 "version": "1.30.0", 8955 "sha256": "12ap7376fpr76hjamswca0h2z48k791gs8fmw5kba56ngsypr1f6", 8956 "depends": ["Biobase", "GSEABase", "XML", "digest", "foreach", "iterators", "repo", "rhdf5"] 8957 }, 8958 "getDEE2": { 8959 "name": "getDEE2", 8960 "version": "1.20.0", 8961 "sha256": "0pqbyvj5063xn048x38yg9zpvzg82r4ksbmj4a0gx4cxpw2g4cyf", 8962 "depends": ["SummarizedExperiment", "htm2txt"] 8963 }, 8964 "geva": { 8965 "name": "geva", 8966 "version": "1.18.0", 8967 "sha256": "0pj4dxfqkas5zd71310q32y4r5msd4984rrc2f6xaxhd8dip3cgs", 8968 "depends": ["dbscan", "fastcluster", "matrixStats"] 8969 }, 8970 "geyser": { 8971 "name": "geyser", 8972 "version": "1.2.0", 8973 "sha256": "146avnl23jsn2r19r3ynqqrkkpsghkix738zbac9dqfz3yd7g44x", 8974 "depends": ["BiocStyle", "ComplexHeatmap", "DT", "SummarizedExperiment", "bslib", "dplyr", "ggbeeswarm", "ggplot2", "htmltools", "magrittr", "shiny", "tibble", "tidyr", "tidyselect"] 8975 }, 8976 "gg4way": { 8977 "name": "gg4way", 8978 "version": "1.8.0", 8979 "sha256": "0v9hldgi84k99smaycrfq36simzs7dwfa5c2a3qf1dfbz9ia9ksl", 8980 "depends": ["DESeq2", "dplyr", "edgeR", "ggplot2", "ggrepel", "glue", "janitor", "limma", "magrittr", "purrr", "rlang", "scales", "stringr", "tibble", "tidyr"] 8981 }, 8982 "ggbio": { 8983 "name": "ggbio", 8984 "version": "1.58.0", 8985 "sha256": "0wnscz1r9khbh6lha55025s5wkvs2i3z4v1cjz0v3gkgkva545ff", 8986 "depends": ["AnnotationDbi", "AnnotationFilter", "BSgenome", "Biobase", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Hmisc", "IRanges", "OrganismDbi", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "biovizBase", "ensembldb", "ggplot2", "gridExtra", "gtable", "reshape2", "rlang", "rtracklayer", "scales"] 8987 }, 8988 "ggcyto": { 8989 "name": "ggcyto", 8990 "version": "1.38.0", 8991 "sha256": "0gpqwg8f2pwb9z9rjdmiy6x60zry2wwlf5xq44scv5dm6l2jfapw", 8992 "depends": ["RColorBrewer", "data_table", "flowCore", "flowWorkspace", "ggplot2", "gridExtra", "hexbin", "ncdfFlow", "plyr", "rlang", "scales"] 8993 }, 8994 "ggkegg": { 8995 "name": "ggkegg", 8996 "version": "1.8.0", 8997 "sha256": "1imcszvrg3z9vsn63hnsdwyl35dspvxvmjd9rfrgz6w8v677firx", 8998 "depends": ["BiocFileCache", "XML", "data_table", "dplyr", "ggplot2", "ggraph", "gtable", "igraph", "magick", "patchwork", "shadowtext", "stringr", "tibble", "tidygraph"] 8999 }, 9000 "ggmanh": { 9001 "name": "ggmanh", 9002 "version": "1.14.0", 9003 "sha256": "0r9v6ss9hp9y729vcw9c4sw7diclv337z38hp9fxz4ys3vp68ck2", 9004 "depends": ["RColorBrewer", "SeqArray", "dplyr", "gdsfmt", "ggplot2", "ggrepel", "magrittr", "paletteer", "pals", "rlang", "scales", "tidyr"] 9005 }, 9006 "ggmsa": { 9007 "name": "ggmsa", 9008 "version": "1.16.0", 9009 "sha256": "0wf0rvqn7q716hp3m53mc425rzjmhj14ajz0by3rx0ix357y7xg2", 9010 "depends": ["Biostrings", "R4RNA", "RColorBrewer", "aplot", "dplyr", "ggforce", "ggfun", "ggplot2", "ggtree", "magrittr", "seqmagick", "tidyr"] 9011 }, 9012 "ggsc": { 9013 "name": "ggsc", 9014 "version": "1.8.0", 9015 "sha256": "1bxkf3blwvgpwa3s861i4mg6x6ny6kq27wgn9abpdi2k12545m8s", 9016 "depends": ["RColorBrewer", "Rcpp", "RcppArmadillo", "RcppParallel", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "cli", "dplyr", "ggfun", "ggplot2", "rlang", "scales", "scattermore", "tibble", "tidydr", "tidyr", "yulab_utils"] 9017 }, 9018 "ggseqalign": { 9019 "name": "ggseqalign", 9020 "version": "1.4.0", 9021 "sha256": "013a1gda7hwmyis0zs4ajaz42phwlnji2lqynasysy764nknlznh", 9022 "depends": ["dplyr", "ggplot2", "pwalign"] 9023 }, 9024 "ggspavis": { 9025 "name": "ggspavis", 9026 "version": "1.16.0", 9027 "sha256": "1xnmajaxc1k3am1p2fkf56l6pdv5ayn0pqivyz3x7fp2yix0wxn4", 9028 "depends": ["RColorBrewer", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "ggrepel", "ggside", "scales"] 9029 }, 9030 "ggtree": { 9031 "name": "ggtree", 9032 "version": "4.0.1", 9033 "sha256": "0vk1l1jmw4acgmpmgcx0pz7j39yp391mba8q1xnc8rmlfw51qvxj", 9034 "depends": ["ape", "aplot", "cli", "dplyr", "ggfun", "ggiraph", "ggplot2", "magrittr", "purrr", "rlang", "scales", "tidyr", "tidytree", "treeio", "yulab_utils"] 9035 }, 9036 "ggtreeDendro": { 9037 "name": "ggtreeDendro", 9038 "version": "1.12.0", 9039 "sha256": "0pc5lrc0p5d1yr6yrazz82z87h0zix8an19vjncw5pp3gyjs2z5g", 9040 "depends": ["ggplot2", "ggtree", "tidytree"] 9041 }, 9042 "ggtreeExtra": { 9043 "name": "ggtreeExtra", 9044 "version": "1.20.0", 9045 "sha256": "086j86xxf8xn4kqkgs6b3r2zyrngi2inhhabj47c5mcyxy7cbddz", 9046 "depends": ["cli", "ggnewscale", "ggplot2", "ggtree", "magrittr", "rlang", "tidytree"] 9047 }, 9048 "ggtreeSpace": { 9049 "name": "ggtreeSpace", 9050 "version": "1.6.0", 9051 "sha256": "0yy7hap224hznl4g9nj0bn0rf57snwbrw419b14l2h5rg5gi5fc5", 9052 "depends": ["GGally", "ape", "dplyr", "ggplot2", "ggtree", "interp", "phytools", "rlang", "tibble", "tidyr", "tidyselect"] 9053 }, 9054 "ginmappeR": { 9055 "name": "ginmappeR", 9056 "version": "1.6.0", 9057 "sha256": "0x85rkhs46bln7bd51lz1vqx4nd3qg83vkvg1bnb9755k7rz3x58", 9058 "depends": ["KEGGREST", "UniProt_ws", "XML", "cachem", "httr", "jsonlite", "memoise", "rentrez", "rvest"] 9059 }, 9060 "glmGamPoi": { 9061 "name": "glmGamPoi", 9062 "version": "1.22.0", 9063 "sha256": "1i9sy6a47ynb3lghi2mghk6mvgbr3kny6c3n208lxqb4b7si1f1z", 9064 "depends": ["BiocGenerics", "DelayedArray", "DelayedMatrixStats", "HDF5Array", "Matrix", "MatrixGenerics", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "assorthead", "beachmat", "matrixStats", "rlang", "vctrs"] 9065 }, 9066 "glmSparseNet": { 9067 "name": "glmSparseNet", 9068 "version": "1.28.0", 9069 "sha256": "0qxss4zfdds590ldfdrhn8c6brd9z8pknp462jw2p0bjz8wvm8lp", 9070 "depends": ["Matrix", "MultiAssayExperiment", "SummarizedExperiment", "TCGAutils", "biomaRt", "checkmate", "dplyr", "forcats", "futile_logger", "ggplot2", "glmnet", "glue", "httr", "lifecycle", "readr", "rlang", "survminer"] 9071 }, 9072 "globalSeq": { 9073 "name": "globalSeq", 9074 "version": "1.38.0", 9075 "sha256": "0i6i0hj733z2d8xqwg1nm1dyp3h5p32rdxmnxp4qgzwk96vz8b51", 9076 "depends": [] 9077 }, 9078 "globaltest": { 9079 "name": "globaltest", 9080 "version": "5.64.0", 9081 "sha256": "064ffcfk9sxmjii1pyl5nsbdr116blvvi3l46chvrvfjjd5z8sfn", 9082 "depends": ["AnnotationDbi", "Biobase", "annotate", "survival"] 9083 }, 9084 "gmapR": { 9085 "name": "gmapR", 9086 "version": "1.51.1", 9087 "sha256": "0y2gh8mqkdcciag09vb1fz9i32d8j3hj3frji7j644xpd2hr12ks", 9088 "depends": ["BSgenome", "Biobase", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "VariantAnnotation", "rtracklayer"] 9089 }, 9090 "gmoviz": { 9091 "name": "gmoviz", 9092 "version": "1.22.0", 9093 "sha256": "0ggy20alp14129d477zywhjj3jl8396wc1sfc8k0gb3hnzb08x9f", 9094 "depends": ["BiocGenerics", "Biostrings", "ComplexHeatmap", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "circlize", "colorspace", "gridBase", "pracma", "rtracklayer"] 9095 }, 9096 "goProfiles": { 9097 "name": "goProfiles", 9098 "version": "1.72.0", 9099 "sha256": "0wkkcwr9cz0a2vlwal1i33zr1m5m0s8h9nal2jp97yhfr82c30hm", 9100 "depends": ["AnnotationDbi", "Biobase", "CompQuadForm", "GO_db", "stringr"] 9101 }, 9102 "goSTAG": { 9103 "name": "goSTAG", 9104 "version": "1.34.0", 9105 "sha256": "1c1n7q1f52x6sd1l3772zq32bvkbwa4ffa82c09laca2hmydfaws", 9106 "depends": ["AnnotationDbi", "GO_db", "biomaRt", "memoise"] 9107 }, 9108 "goSorensen": { 9109 "name": "goSorensen", 9110 "version": "1.12.0", 9111 "sha256": "0md7w06mlnalcfpmsg4b3x3cmvy8xx8smwvq2vfvp3fyfghx1q9y", 9112 "depends": ["clusterProfiler", "goProfiles", "org_Hs_eg_db", "stringr"] 9113 }, 9114 "goTools": { 9115 "name": "goTools", 9116 "version": "1.84.0", 9117 "sha256": "01jgq12iskpdp8s4sf3ndk16n99ypwrfw61l8jjfvlla2nw73lpa", 9118 "depends": ["AnnotationDbi", "GO_db"] 9119 }, 9120 "goseq": { 9121 "name": "goseq", 9122 "version": "1.62.0", 9123 "sha256": "1p8vbisgdv4cmb47kr6x7nycm3j9sf3y5ib6lcq2i9y0c49ddrz2", 9124 "depends": ["AnnotationDbi", "BiasedUrn", "BiocGenerics", "GO_db", "GenomicFeatures", "Seqinfo", "geneLenDataBase", "mgcv", "rtracklayer"] 9125 }, 9126 "gpls": { 9127 "name": "gpls", 9128 "version": "1.82.0", 9129 "sha256": "0kn2vxsl379qh2gs7am46fzn2c44kgj46n6g49b94a7vgjrwm2qi", 9130 "depends": [] 9131 }, 9132 "graper": { 9133 "name": "graper", 9134 "version": "1.26.0", 9135 "sha256": "0n9z7ni769yylrq22dp2saka55ymm178ind9dvr7h3bhrb9v34kf", 9136 "depends": ["BH", "Matrix", "Rcpp", "RcppArmadillo", "cowplot", "ggplot2", "matrixStats"] 9137 }, 9138 "graph": { 9139 "name": "graph", 9140 "version": "1.88.0", 9141 "sha256": "1sxn2h83j3qawp9jwpg63g50px2gk5dmlmdy6a7jwx3hb44sppbm", 9142 "depends": ["BiocGenerics"] 9143 }, 9144 "graphite": { 9145 "name": "graphite", 9146 "version": "1.56.0", 9147 "sha256": "0481mc4h33n8kky5qph2isjibfclcc694k8pxlf6aijq6hbqxc78", 9148 "depends": ["AnnotationDbi", "dir_expiry", "graph", "httr", "lifecycle", "purrr", "rappdirs", "rlang"] 9149 }, 9150 "groHMM": { 9151 "name": "groHMM", 9152 "version": "1.44.0", 9153 "sha256": "0xdma6zx4sdkqfbs4v8ipxa38xywmdlgbdmihl0zysp6nxmm1jvg", 9154 "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "Seqinfo", "rtracklayer"] 9155 }, 9156 "gscreend": { 9157 "name": "gscreend", 9158 "version": "1.24.0", 9159 "sha256": "0gf3mv57c4f93xq75fyd9xqzkwn8yrz5x4sxpr8f5bxxriwdyd55", 9160 "depends": ["BiocParallel", "SummarizedExperiment", "fGarch", "nloptr"] 9161 }, 9162 "gsean": { 9163 "name": "gsean", 9164 "version": "1.30.0", 9165 "sha256": "07k0b722i33dyrw65iv0ami4kxjxd7gzcnrn10yk9yam187g0hnp", 9166 "depends": ["PPInfer", "fgsea"] 9167 }, 9168 "gtrellis": { 9169 "name": "gtrellis", 9170 "version": "1.42.0", 9171 "sha256": "0lbqzdfz7ylw066ng01vvm5azvnjfxhhbfcjk6y0l5xbs2c5ckac", 9172 "depends": ["GenomicRanges", "GetoptLong", "IRanges", "circlize"] 9173 }, 9174 "gwascat": { 9175 "name": "gwascat", 9176 "version": "2.42.0", 9177 "sha256": "1v5z4fmwgs3swvpa09y986sracz0nsggq8s9hp1nmwb9a9grw8px", 9178 "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "VariantAnnotation", "data_table", "readr", "snpStats", "tibble"] 9179 }, 9180 "gwasurvivr": { 9181 "name": "gwasurvivr", 9182 "version": "1.28.0", 9183 "sha256": "0p6h5594ysscazipf5va545mj36vkbw4dprqsqhg21ih411bqk9r", 9184 "depends": ["GWASTools", "SNPRelate", "SummarizedExperiment", "VariantAnnotation", "matrixStats", "survival"] 9185 }, 9186 "gypsum": { 9187 "name": "gypsum", 9188 "version": "1.6.0", 9189 "sha256": "0wn6mxdkr1msys9n3799qplmvpr9b8qjzhw1magahndidsylz8pf", 9190 "depends": ["filelock", "httr2", "jsonlite", "rappdirs"] 9191 }, 9192 "h5mread": { 9193 "name": "h5mread", 9194 "version": "1.2.0", 9195 "sha256": "01iykyb36cnzbs7xf3jcgnndnib4pk0w4wg8scy1rnagcy89yp2a", 9196 "depends": ["BiocGenerics", "IRanges", "Rhdf5lib", "S4Arrays", "S4Vectors", "SparseArray", "rhdf5", "rhdf5filters"] 9197 }, 9198 "h5vc": { 9199 "name": "h5vc", 9200 "version": "2.44.0", 9201 "sha256": "0a2ali36kigkn65a5gb11xid2c28432l3hvdkjf27h4z7jl1cv16", 9202 "depends": ["BatchJobs", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rhtslib", "Rsamtools", "S4Vectors", "abind", "ggplot2", "gridExtra", "h5vcData", "reshape", "rhdf5"] 9203 }, 9204 "hapFabia": { 9205 "name": "hapFabia", 9206 "version": "1.52.0", 9207 "sha256": "1asxg02xrvqsx1vnyh14nd3xfsk8q0fi95w65c97dknrnhy1c2wl", 9208 "depends": ["Biobase", "fabia"] 9209 }, 9210 "hdxmsqc": { 9211 "name": "hdxmsqc", 9212 "version": "1.6.0", 9213 "sha256": "03r8k913p3f4024jr6r5nd872ixxqfkhwngi2g930vw4j53y04k3", 9214 "depends": ["BiocStyle", "MsCoreUtils", "QFeatures", "S4Vectors", "Spectra", "dplyr", "ggplot2", "knitr", "tidyr"] 9215 }, 9216 "heatmaps": { 9217 "name": "heatmaps", 9218 "version": "1.34.0", 9219 "sha256": "1656vvcqjpiwibxqvlx0ysalnc53xifkh9ypb7j3prdpc7k243nx", 9220 "depends": ["BiocGenerics", "Biostrings", "EBImage", "GenomicRanges", "IRanges", "KernSmooth", "Matrix", "RColorBrewer", "Seqinfo", "plotrix"] 9221 }, 9222 "hermes": { 9223 "name": "hermes", 9224 "version": "1.14.0", 9225 "sha256": "0ylqg4jhsv1qqd2663jskn2r1m6f79snx0pisn8i3p6yh7n2cpi8", 9226 "depends": ["Biobase", "BiocGenerics", "ComplexHeatmap", "DESeq2", "EnvStats", "GenomicRanges", "IRanges", "MultiAssayExperiment", "R6", "Rdpack", "S4Vectors", "SummarizedExperiment", "assertthat", "biomaRt", "checkmate", "circlize", "dplyr", "edgeR", "forcats", "ggfortify", "ggplot2", "ggrepel", "limma", "magrittr", "matrixStats", "purrr", "rlang", "tidyr"] 9227 }, 9228 "hicVennDiagram": { 9229 "name": "hicVennDiagram", 9230 "version": "1.8.0", 9231 "sha256": "11fc1ykmk0g5gpjxi195hqw2cxn212asarmj0pjcvjzh30k4i12d", 9232 "depends": ["ComplexUpset", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "Seqinfo", "eulerr", "ggplot2", "htmlwidgets", "reshape2", "rtracklayer", "svglite"] 9233 }, 9234 "hierGWAS": { 9235 "name": "hierGWAS", 9236 "version": "1.40.0", 9237 "sha256": "0l58pcyhgxnc56j9gbp6dlw97apa2r67xcvli76ldk1mwpf0hxnb", 9238 "depends": ["fastcluster", "fmsb", "glmnet"] 9239 }, 9240 "hierinf": { 9241 "name": "hierinf", 9242 "version": "1.28.0", 9243 "sha256": "1k5i6k6wbz43mf7nsg48idykxr7mi42nc6qmsmpvcj863nkdhm89", 9244 "depends": ["fmsb", "glmnet"] 9245 }, 9246 "hmdbQuery": { 9247 "name": "hmdbQuery", 9248 "version": "1.30.0", 9249 "sha256": "1zasi8mb3pi5yxz2w7v7b5zwmkb8syl0ir41gafz0mq9pab3yj3a", 9250 "depends": ["S4Vectors", "XML"] 9251 }, 9252 "hoodscanR": { 9253 "name": "hoodscanR", 9254 "version": "1.8.0", 9255 "sha256": "1fxf2zixbcz5g6nncgkdbiz4gb4iv2d085jz1li8cd6l2fxsyab1", 9256 "depends": ["ComplexHeatmap", "RANN", "Rcpp", "SpatialExperiment", "SummarizedExperiment", "circlize", "ggplot2", "knitr", "rlang", "rmarkdown", "scico"] 9257 }, 9258 "hopach": { 9259 "name": "hopach", 9260 "version": "2.70.0", 9261 "sha256": "00xbm6lld8w711x226rms020zpn0wi2ri7q59iwg4w4xmdjqq8xh", 9262 "depends": ["Biobase", "BiocGenerics", "cluster"] 9263 }, 9264 "hpar": { 9265 "name": "hpar", 9266 "version": "1.52.0", 9267 "sha256": "1png19c1dr2banwc07azwz0rxrkw9820vkj8362syv4dryphx3c5", 9268 "depends": ["ExperimentHub"] 9269 }, 9270 "hummingbird": { 9271 "name": "hummingbird", 9272 "version": "1.20.0", 9273 "sha256": "1aiv1aavc6al6hv05828alqmnf6q8af126aa3na3m0zvfjvaf2fa", 9274 "depends": ["GenomicRanges", "IRanges", "Rcpp", "SummarizedExperiment"] 9275 }, 9276 "hyperdraw": { 9277 "name": "hyperdraw", 9278 "version": "1.62.0", 9279 "sha256": "07k1vkqilvy83ijawlw038dqq89plmjv5paz6k1mjif8f730lkgl", 9280 "depends": ["Rgraphviz", "graph", "hypergraph"] 9281 }, 9282 "hypergraph": { 9283 "name": "hypergraph", 9284 "version": "1.82.0", 9285 "sha256": "0326ypzscnv2xpyvpigwsanp065wiply8w6ydg1gvryc1in5dlbm", 9286 "depends": ["graph"] 9287 }, 9288 "iASeq": { 9289 "name": "iASeq", 9290 "version": "1.54.0", 9291 "sha256": "04rxy267kymkbiqjv818hhb8lxh1l4hk9pxw4psr0q527iz6rrj0", 9292 "depends": [] 9293 }, 9294 "iBBiG": { 9295 "name": "iBBiG", 9296 "version": "1.54.0", 9297 "sha256": "1m9kdnpa34a9y3sdh7a53clpq9zc4cl5zx7rnrsm0998bfrbwwpk", 9298 "depends": ["ade4", "biclust", "xtable"] 9299 }, 9300 "iBMQ": { 9301 "name": "iBMQ", 9302 "version": "1.50.0", 9303 "sha256": "1n05qnr3kfnbm5ns2kich5n9xbhy7rhlyfwx001mbinhihwf7cyb", 9304 "depends": ["Biobase", "ggplot2"] 9305 }, 9306 "iCARE": { 9307 "name": "iCARE", 9308 "version": "1.38.0", 9309 "sha256": "0rj33c22rssznqi8jayg2lnhx2adwina6ic2nswmq1kvd9zcdf6x", 9310 "depends": ["Hmisc", "gtools", "plotrix"] 9311 }, 9312 "iCNV": { 9313 "name": "iCNV", 9314 "version": "1.30.0", 9315 "sha256": "0hkxikinkbpdgg7l7n0v0lyazd09i2n92dx0gakfvrd7bn3v6dql", 9316 "depends": ["CODEX", "data_table", "dplyr", "fields", "ggplot2", "rlang", "tidyr", "truncnorm"] 9317 }, 9318 "iCOBRA": { 9319 "name": "iCOBRA", 9320 "version": "1.38.0", 9321 "sha256": "0fyls8ckgbkh71ik9m475nlf51p1giby6d5qrrjjzg59bwhbksjm", 9322 "depends": ["DT", "ROCR", "UpSetR", "dplyr", "ggplot2", "limma", "reshape2", "rlang", "scales", "shiny", "shinyBS", "shinydashboard"] 9323 }, 9324 "iCheck": { 9325 "name": "iCheck", 9326 "version": "1.40.0", 9327 "sha256": "0f9vhavj849syn1kdsiij120s3w97y7sqiv4qnpyp5r1s4k75bfl", 9328 "depends": ["Biobase", "GeneSelectMMD", "MASS", "affy", "gplots", "limma", "lmtest", "lumi", "preprocessCore", "randomForest", "rgl", "scatterplot3d"] 9329 }, 9330 "iChip": { 9331 "name": "iChip", 9332 "version": "1.64.0", 9333 "sha256": "1hkgxj54nw4g3fal6r94nkr3j4ixv0c5wi6g2y7hx5bx6mmablmj", 9334 "depends": ["limma"] 9335 }, 9336 "iClusterPlus": { 9337 "name": "iClusterPlus", 9338 "version": "1.46.0", 9339 "sha256": "1bqi0hckfphs7ixb0mh67a8q9q43fxs3n36bvgrhgpari4gl9axz", 9340 "depends": [] 9341 }, 9342 "iGC": { 9343 "name": "iGC", 9344 "version": "1.40.0", 9345 "sha256": "0jli4qyzyypkk43kk58122dmibjnb09gpks1yfgqpqczna2h46xc", 9346 "depends": ["data_table", "plyr"] 9347 }, 9348 "iModMix": { 9349 "name": "iModMix", 9350 "version": "1.0.0", 9351 "sha256": "0kif27wq4m1qsrv34zla4w0wlmdlsi6z8v54mz10p101lrvppnfk", 9352 "depends": ["ComplexHeatmap", "DT", "ExperimentHub", "RColorBrewer", "SummarizedExperiment", "WGCNA", "config", "corrplot", "cowplot", "dplyr", "dynamicTreeCut", "ggplot2", "glassoFast", "golem", "httr", "iModMixData", "impute", "purrr", "shiny", "shinyBS", "stringr", "tidyr", "visNetwork"] 9353 }, 9354 "iSEE": { 9355 "name": "iSEE", 9356 "version": "2.22.0", 9357 "sha256": "1g4mcvc7qb04cy307lhd11pxshq81s84b87dcyylqasibhxmbjyp", 9358 "depends": ["BiocGenerics", "ComplexHeatmap", "DT", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circlize", "colourpicker", "ggplot2", "ggrepel", "igraph", "listviewer", "mgcv", "rintrojs", "shiny", "shinyAce", "shinyWidgets", "shinydashboard", "shinyjs", "vipor", "viridisLite"] 9359 }, 9360 "iSEEde": { 9361 "name": "iSEEde", 9362 "version": "1.8.0", 9363 "sha256": "0csm53kjgdg6ca42w36gfcs2c8x4bvl06ngnhqaa1hg9bx3nn4bl", 9364 "depends": ["DESeq2", "S4Vectors", "SummarizedExperiment", "edgeR", "iSEE", "shiny"] 9365 }, 9366 "iSEEfier": { 9367 "name": "iSEEfier", 9368 "version": "1.6.0", 9369 "sha256": "0vqrm2zm8dmrrgj7lh8m8kx6h97ii6f39m3mi7i2h1nklihkz54s", 9370 "depends": ["BiocBaseUtils", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "iSEE", "iSEEu", "igraph", "rlang", "visNetwork"] 9371 }, 9372 "iSEEhex": { 9373 "name": "iSEEhex", 9374 "version": "1.12.0", 9375 "sha256": "1dm7j0159c52a4smhwq18da78fl8rfzibvr5dq2rmdgfvk3xg27p", 9376 "depends": ["SummarizedExperiment", "ggplot2", "hexbin", "iSEE", "shiny"] 9377 }, 9378 "iSEEhub": { 9379 "name": "iSEEhub", 9380 "version": "1.12.0", 9381 "sha256": "0gjz3r0slzzdsdycnq6vlcai4l3qmw4xx25b0id4va5224j1pbld", 9382 "depends": ["AnnotationHub", "BiocManager", "DT", "ExperimentHub", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "iSEE", "rintrojs", "shiny", "shinydashboard", "shinyjs"] 9383 }, 9384 "iSEEindex": { 9385 "name": "iSEEindex", 9386 "version": "1.8.0", 9387 "sha256": "1id3hbc24lvk4lhfm2l75n0hd1l37hl6v70cbbb8kh6kdfmhidy3", 9388 "depends": ["BiocFileCache", "DT", "SingleCellExperiment", "SummarizedExperiment", "iSEE", "paws_storage", "rintrojs", "shiny", "shinydashboard", "shinyjs", "stringr", "urltools"] 9389 }, 9390 "iSEEpathways": { 9391 "name": "iSEEpathways", 9392 "version": "1.8.0", 9393 "sha256": "06dy4s9sn2pm2q8xh20p83nv1km1f6xcp3radxq8cwy4jw3j5rzw", 9394 "depends": ["S4Vectors", "SummarizedExperiment", "ggplot2", "iSEE", "shiny", "shinyWidgets"] 9395 }, 9396 "iSEEtree": { 9397 "name": "iSEEtree", 9398 "version": "1.4.0", 9399 "sha256": "1j5p859lsjjv831wkhdmkwhw61g3yw1ynayz1ww8vbh0b3kchqa0", 9400 "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "ggplot2", "ggtree", "iSEE", "mia", "miaViz", "purrr", "shiny", "shinyWidgets", "tidygraph"] 9401 }, 9402 "iSEEu": { 9403 "name": "iSEEu", 9404 "version": "1.22.0", 9405 "sha256": "1gdbqff3j3s8793wn26c59zms1vahvskvhka1rzp5fqd7i09a9id", 9406 "depends": ["DT", "IRanges", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "colourpicker", "ggplot2", "iSEE", "iSEEhex", "shiny", "shinyAce"] 9407 }, 9408 "iSeq": { 9409 "name": "iSeq", 9410 "version": "1.62.0", 9411 "sha256": "118g683pbn713g5iqrdsipbfnwi73kn80pq0ir8ignx7jn36vp12", 9412 "depends": [] 9413 }, 9414 "iasva": { 9415 "name": "iasva", 9416 "version": "1.28.0", 9417 "sha256": "0lkyfgwr2prar7gzf1dn8a8q81d3al2hq9pyhjcn7ghpjpwrw1mx", 9418 "depends": ["BiocParallel", "SummarizedExperiment", "cluster", "irlba"] 9419 }, 9420 "ibh": { 9421 "name": "ibh", 9422 "version": "1.58.0", 9423 "sha256": "0nljjvapwfdy07w3zg35znyh2k645bn8psfnl84dxr4hmq3g51ra", 9424 "depends": ["simpIntLists"] 9425 }, 9426 "icetea": { 9427 "name": "icetea", 9428 "version": "1.28.0", 9429 "sha256": "0f0w294bqmrh4a5gsyfiv9228734cv5ybskazgzsnjvbndlhk69p", 9430 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "TxDb_Dmelanogaster_UCSC_dm6_ensGene", "VariantAnnotation", "csaw", "edgeR", "ggplot2", "limma", "rtracklayer"] 9431 }, 9432 "ideal": { 9433 "name": "ideal", 9434 "version": "2.4.0", 9435 "sha256": "1h8yvw4rwsbv30vny8rw6df99v5mj7l6cbm5fgxgl29hlb1hcd6j", 9436 "depends": ["AnnotationDbi", "BiocParallel", "DESeq2", "DT", "GO_db", "GOstats", "GenomicRanges", "IHW", "IRanges", "S4Vectors", "SummarizedExperiment", "UpSetR", "base64enc", "dplyr", "ggplot2", "ggrepel", "goseq", "gplots", "heatmaply", "knitr", "limma", "mosdef", "pheatmap", "plotly", "rentrez", "rintrojs", "rlang", "rmarkdown", "shiny", "shinyAce", "shinyBS", "shinydashboard", "stringr", "topGO"] 9437 }, 9438 "idiogram": { 9439 "name": "idiogram", 9440 "version": "1.86.0", 9441 "sha256": "0d9m9x7gsx1ywcf1pk7ssp4gal29i833qjaqq4bx1ihrlr75nf06", 9442 "depends": ["Biobase", "annotate", "plotrix"] 9443 }, 9444 "idpr": { 9445 "name": "idpr", 9446 "version": "1.20.0", 9447 "sha256": "0mbk2zpmjksp6a59wm4bhf9k9v9zblyydjj231zpga6vslybx3g3", 9448 "depends": ["Biostrings", "dplyr", "ggplot2", "jsonlite", "magrittr", "plyr", "rlang"] 9449 }, 9450 "idr2d": { 9451 "name": "idr2d", 9452 "version": "1.24.0", 9453 "sha256": "0vm8ax9f6q8zzwggrcxy5gf62ikfhlp2mybr9zg74w99zgbyabx6", 9454 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "dplyr", "futile_logger", "ggplot2", "idr", "magrittr", "reticulate", "scales", "stringr"] 9455 }, 9456 "igblastr": { 9457 "name": "igblastr", 9458 "version": "1.0.0", 9459 "sha256": "1vjlqjiczdfq0wdbjjb3knpa3xqibqz08r06qyqvnvvs533axl5r", 9460 "depends": ["Biostrings", "GenomeInfoDb", "IRanges", "R_utils", "S4Vectors", "curl", "httr", "jsonlite", "rvest", "tibble", "xml2", "xtable"] 9461 }, 9462 "igvR": { 9463 "name": "igvR", 9464 "version": "1.30.0", 9465 "sha256": "0ia9vx40djl3lmlpirp7knjygd2zsimpn471ydjqw09bamxyin8k", 9466 "depends": ["BiocGenerics", "BrowserViz", "GenomicAlignments", "GenomicRanges", "RColorBrewer", "VariantAnnotation", "httpuv", "httr", "rtracklayer"] 9467 }, 9468 "igvShiny": { 9469 "name": "igvShiny", 9470 "version": "1.6.0", 9471 "sha256": "05xd8ydk4z4xqgdw626jk3cfnbk9f9nv6cv6n4i0wg9vy6r87wza", 9472 "depends": ["BiocGenerics", "GenomeInfoDbData", "GenomicRanges", "checkmate", "futile_logger", "htmlwidgets", "httr", "jsonlite", "randomcoloR", "shiny"] 9473 }, 9474 "illuminaio": { 9475 "name": "illuminaio", 9476 "version": "0.52.0", 9477 "sha256": "0hcn43ipy0dijr3kqdcn8hpv3a5y1xmg8d7aa2hd7i7ipjh5bfhf", 9478 "depends": ["base64"] 9479 }, 9480 "imageTCGA": { 9481 "name": "imageTCGA", 9482 "version": "1.2.0", 9483 "sha256": "15wd10s1xcmkfqyd92m25lgcy6hnizrhvl7vnajgrp0g512s7jg6", 9484 "depends": ["DT", "bsicons", "bslib", "clipr", "dplyr", "ggplot2", "leaflet", "rlang", "shiny", "tidyr", "viridis"] 9485 }, 9486 "imcRtools": { 9487 "name": "imcRtools", 9488 "version": "1.16.0", 9489 "sha256": "07a5p6r5rycp55gs6iaqkqy7wgvajs5x0806qc3fidg0v118qfp0", 9490 "depends": ["BiocNeighbors", "BiocParallel", "DT", "EBImage", "MatrixGenerics", "RTriangle", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "abind", "concaveman", "cytomapper", "data_table", "distances", "dplyr", "ggplot2", "ggraph", "igraph", "magrittr", "pheatmap", "readr", "rlang", "scuttle", "sf", "stringr", "tidygraph", "tidyselect", "viridis", "vroom"] 9491 }, 9492 "immApex": { 9493 "name": "immApex", 9494 "version": "1.4.0", 9495 "sha256": "0xwj70fgfhqilc4clm54lj7h1q1742339z44nwbl1sjh049x388f", 9496 "depends": ["Matrix", "Rcpp", "SingleCellExperiment", "hash", "httr", "matrixStats", "rvest", "stringr"] 9497 }, 9498 "immunoClust": { 9499 "name": "immunoClust", 9500 "version": "1.42.0", 9501 "sha256": "1l6iyf23kvk02zl49hq2y761hg102gv4vf6xzgck6xgp80d2cl9d", 9502 "depends": ["flowCore", "lattice"] 9503 }, 9504 "immunogenViewer": { 9505 "name": "immunogenViewer", 9506 "version": "1.4.0", 9507 "sha256": "03k4sc032nn5siciv41310hcfs7dfjgps50jprpgjbmx3z2zvwgj", 9508 "depends": ["UniProt_ws", "ggplot2", "httr", "jsonlite", "patchwork"] 9509 }, 9510 "immunotation": { 9511 "name": "immunotation", 9512 "version": "1.18.0", 9513 "sha256": "031gl7sckwkrdhnzbadnnlxqfi48nc2wm9x2zdzw6qds39hg8ay1", 9514 "depends": ["curl", "ggplot2", "maps", "ontologyIndex", "readr", "rlang", "rvest", "stringr", "tidyr", "xml2"] 9515 }, 9516 "impute": { 9517 "name": "impute", 9518 "version": "1.84.0", 9519 "sha256": "1lcyfwgs7pq1qwnglgqp7gs3rxymxgv08jmgq56xd1qjr9rz4dl6", 9520 "depends": [] 9521 }, 9522 "infercnv": { 9523 "name": "infercnv", 9524 "version": "1.26.0", 9525 "sha256": "1gkgvkj06kpqwl573d5l8d9bsdp7nq61m688ma9d2fx6wg4a9r7l", 9526 "depends": ["BiocGenerics", "HiddenMarkov", "Matrix", "RANN", "RColorBrewer", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "ape", "argparse", "caTools", "coda", "coin", "digest", "doParallel", "dplyr", "edgeR", "fastcluster", "fitdistrplus", "foreach", "futile_logger", "future", "ggplot2", "gplots", "gridExtra", "igraph", "parallelDist", "phyclust", "reshape2", "rjags", "tidyr"] 9527 }, 9528 "infinityFlow": { 9529 "name": "infinityFlow", 9530 "version": "1.20.0", 9531 "sha256": "010wv8nm1hjpr7f2y1z3bv7mbjbzlr84id7qmmhgkp6b0gmkwmgp", 9532 "depends": ["Biobase", "flowCore", "generics", "gtools", "matlab", "pbapply", "png", "raster", "uwot", "xgboost"] 9533 }, 9534 "intansv": { 9535 "name": "intansv", 9536 "version": "1.50.0", 9537 "sha256": "1zmb28d8zkg58d3yrbgj9aqac6zyr9l03gryyxsz2yadwkngpyh4", 9538 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "ggbio", "plyr"] 9539 }, 9540 "interacCircos": { 9541 "name": "interacCircos", 9542 "version": "1.20.0", 9543 "sha256": "12nc76sgidbak7dwhjxrzjzc07yi6jn44g7zvaq1mld93i0hds08", 9544 "depends": ["RColorBrewer", "htmlwidgets", "plyr"] 9545 }, 9546 "interactiveDisplay": { 9547 "name": "interactiveDisplay", 9548 "version": "1.48.0", 9549 "sha256": "02amr55nk6jx059a0shrwpnzkgcdfsr2x8k975j7x9y0nwsj6l94", 9550 "depends": ["AnnotationDbi", "BiocGenerics", "Category", "RColorBrewer", "XML", "ggplot2", "gridSVG", "interactiveDisplayBase", "plyr", "reshape2", "shiny"] 9551 }, 9552 "interactiveDisplayBase": { 9553 "name": "interactiveDisplayBase", 9554 "version": "1.48.0", 9555 "sha256": "0slmb7cd9sn0146r1ad0cnaiihh7vh22fx41w7zdnq8c5nykkhad", 9556 "depends": ["BiocGenerics", "DT", "shiny"] 9557 }, 9558 "ipdDb": { 9559 "name": "ipdDb", 9560 "version": "1.28.0", 9561 "sha256": "13w0zgpcfaj2mradn0s95yszlf97b4sp7k4zzjjzfxfzi1xn8q7v", 9562 "depends": ["AnnotationDbi", "AnnotationHub", "Biostrings", "DBI", "GenomicRanges", "IRanges", "RSQLite", "assertthat"] 9563 }, 9564 "iscream": { 9565 "name": "iscream", 9566 "version": "1.0.0", 9567 "sha256": "19azxk53w3nnbjh54hzmznk1ilgck5i6m1m47wl7456fwkay6d3x", 9568 "depends": ["Matrix", "Rcpp", "RcppArmadillo", "RcppProgress", "RcppSpdlog", "Rhtslib", "data_table", "parallelly", "pbapply", "stringfish"] 9569 }, 9570 "islify": { 9571 "name": "islify", 9572 "version": "1.2.0", 9573 "sha256": "0n8585c27fl6zbhwl12nk8n9cc8vchp43rkh2vfmp42w6nslfcm5", 9574 "depends": ["Matrix", "RBioFormats", "abind", "autothresholdr", "dbscan", "png", "tiff"] 9575 }, 9576 "isobar": { 9577 "name": "isobar", 9578 "version": "1.56.0", 9579 "sha256": "1yckivblgrd80j3i186raawlahdm8akkrmmjc8xckcbld4afls0v", 9580 "depends": ["Biobase", "biomaRt", "distr", "ggplot2", "plyr"] 9581 }, 9582 "iterativeBMA": { 9583 "name": "iterativeBMA", 9584 "version": "1.68.0", 9585 "sha256": "1ja588rr6zmghfgi5f4r7hqnh94siw72n90z76wdivw22y90v57p", 9586 "depends": ["BMA", "Biobase", "leaps"] 9587 }, 9588 "iterativeBMAsurv": { 9589 "name": "iterativeBMAsurv", 9590 "version": "1.68.0", 9591 "sha256": "0gqnsy9q43h7brc47xsvxrwmnagvi91pici0xxjsjhbvby5z76qg", 9592 "depends": ["BMA", "leaps", "survival"] 9593 }, 9594 "ivygapSE": { 9595 "name": "ivygapSE", 9596 "version": "1.32.0", 9597 "sha256": "0b9y6iznlpf77dy61hrnz6nhcsr2h8hzw65waqwwwvbwh61n69z8", 9598 "depends": ["S4Vectors", "SummarizedExperiment", "UpSetR", "ggplot2", "hwriter", "plotly", "shiny", "survival", "survminer"] 9599 }, 9600 "jazzPanda": { 9601 "name": "jazzPanda", 9602 "version": "1.2.0", 9603 "sha256": "0bkzi2x4xlaqwn1wjrkmf4vbnqbcqkyvs9mwkxrh5rwg8dq1znw3", 9604 "depends": ["BiocParallel", "BumpyMatrix", "SpatialExperiment", "caret", "doParallel", "dplyr", "foreach", "glmnet", "magrittr", "spatstat_geom"] 9605 }, 9606 "karyoploteR": { 9607 "name": "karyoploteR", 9608 "version": "1.36.0", 9609 "sha256": "0ymrs6mf0sxfczyxyy8nicg5cir7vz4srl2rjdz7h3937rz965yh", 9610 "depends": ["AnnotationDbi", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "VariantAnnotation", "bamsignals", "bezier", "biovizBase", "digest", "memoise", "regioneR", "rtracklayer"] 9611 }, 9612 "katdetectr": { 9613 "name": "katdetectr", 9614 "version": "1.12.0", 9615 "sha256": "1w1wj2mja9wvlq8zsyc9bbnqsfp8hbi1ga792br15gc2dmhdnajx", 9616 "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "Biobase", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rdpack", "S4Vectors", "VariantAnnotation", "changepoint", "changepoint_np", "checkmate", "dplyr", "ggplot2", "ggtext", "maftools", "plyranges", "rlang", "scales", "tibble", "tidyr"] 9617 }, 9618 "kebabs": { 9619 "name": "kebabs", 9620 "version": "1.44.0", 9621 "sha256": "0wkyn73bcvqdljfscdjvjf3z3997k6crr26q38n8g3wd8x3yd672", 9622 "depends": ["Biostrings", "IRanges", "LiblineaR", "Matrix", "Rcpp", "S4Vectors", "XVector", "apcluster", "e1071", "kernlab"] 9623 }, 9624 "keggorthology": { 9625 "name": "keggorthology", 9626 "version": "2.62.0", 9627 "sha256": "01qnwfqqxd741py39qi90dm46i9fvhbdhwvvzirypigy3v1mnlkw", 9628 "depends": ["AnnotationDbi", "DBI", "graph", "hgu95av2_db"] 9629 }, 9630 "kissDE": { 9631 "name": "kissDE", 9632 "version": "1.30.0", 9633 "sha256": "1i7s9nf8vdcm08805njbz6aqy77k7rir0sdq10jc0kk4qvfd857m", 9634 "depends": ["Biobase", "DESeq2", "DSS", "DT", "ade4", "aods3", "doParallel", "factoextra", "foreach", "ggplot2", "gplots", "matrixStats", "shiny", "shinycssloaders"] 9635 }, 9636 "kmcut": { 9637 "name": "kmcut", 9638 "version": "1.4.0", 9639 "sha256": "0kbzkskb4y6bq9hcq68znl3y3g00inwb6sq0wsqkb6rpdsd3lh06", 9640 "depends": ["S4Vectors", "SummarizedExperiment", "doParallel", "foreach", "pracma", "survival"] 9641 }, 9642 "knowYourCG": { 9643 "name": "knowYourCG", 9644 "version": "1.6.0", 9645 "sha256": "0z3xy1jhm4swzjvairkrxb8z9qqmlrjya8ivsd4jq8jvmawq9wjh", 9646 "depends": ["GenomicRanges", "IRanges", "S4Vectors", "dplyr", "ggplot2", "ggrepel", "magrittr", "reshape2", "rlang", "sesameData", "stringr", "tibble", "wheatmap"] 9647 }, 9648 "koinar": { 9649 "name": "koinar", 9650 "version": "1.4.0", 9651 "sha256": "1fdk46bc7c42jdlqij7f0b8rq067pgr3dmvv9fg4n1410irlwd0c", 9652 "depends": ["httr", "jsonlite"] 9653 }, 9654 "ldblock": { 9655 "name": "ldblock", 9656 "version": "1.40.0", 9657 "sha256": "1v47yvbcpcf9z06gfmjsmxrf06pn57fsbmjshq0ypg5p3c3jn81p", 9658 "depends": ["BiocGenerics", "Matrix", "Seqinfo", "httr", "rlang"] 9659 }, 9660 "lefser": { 9661 "name": "lefser", 9662 "version": "1.20.0", 9663 "sha256": "14gmghf65m7s6x6l5nq1bmmfwx76k4kkmvvvx0p6r4ycpk39rccm", 9664 "depends": ["BiocGenerics", "MASS", "S4Vectors", "SummarizedExperiment", "ape", "coin", "dplyr", "forcats", "ggplot2", "ggrepel", "ggtree", "mia", "purrr", "stringr", "testthat", "tibble", "tidyr", "tidyselect", "treeio"] 9665 }, 9666 "lemur": { 9667 "name": "lemur", 9668 "version": "1.8.0", 9669 "sha256": "0v4wcvpj6gdz0qnw72dr6g2bw9nbfr0bfjpn04f7pliz7vnhm568", 9670 "depends": ["BiocGenerics", "BiocNeighbors", "DelayedMatrixStats", "HDF5Array", "Matrix", "MatrixGenerics", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "glmGamPoi", "harmony", "irlba", "limma", "matrixStats", "rlang", "vctrs"] 9671 }, 9672 "les": { 9673 "name": "les", 9674 "version": "1.60.0", 9675 "sha256": "16n5fbifgikh2knjja6a4yqmwy14qxlqcyscs1a8dhs74fz9nyai", 9676 "depends": ["RColorBrewer", "boot", "fdrtool", "gplots"] 9677 }, 9678 "levi": { 9679 "name": "levi", 9680 "version": "1.28.0", 9681 "sha256": "0n31dqr03nc1b9kri8jjh8k19yny83jvv3y8x6fya12gm3vqa124", 9682 "depends": ["DT", "RColorBrewer", "Rcpp", "colorspace", "dplyr", "ggplot2", "httr", "igraph", "knitr", "reshape2", "rmarkdown", "shiny", "shinydashboard", "shinyjs", "testthat", "xml2"] 9683 }, 9684 "lfa": { 9685 "name": "lfa", 9686 "version": "2.10.0", 9687 "sha256": "0hfagl99sf92000ng0wcn88sblzb64mr8b7kfi4zz2q79n9l8b49", 9688 "depends": ["RSpectra", "corpcor"] 9689 }, 9690 "limma": { 9691 "name": "limma", 9692 "version": "3.66.0", 9693 "sha256": "1901p5k4wb7jaifdq8gybiw1sihvr7v3gnf5l4484wrhf2zl3fnq", 9694 "depends": ["statmod"] 9695 }, 9696 "limmaGUI": { 9697 "name": "limmaGUI", 9698 "version": "1.86.0", 9699 "sha256": "1ik0wadac2yvmrcvqk25irmlx0qb8hwlj06lqai2kvnz1x2drfdc", 9700 "depends": ["R2HTML", "limma", "tkrplot", "xtable"] 9701 }, 9702 "limpa": { 9703 "name": "limpa", 9704 "version": "1.2.0", 9705 "sha256": "105gcsf42p91xx213xrfqiywk9hvh9j3dy9bdnp9kmk0ncv4489a", 9706 "depends": ["data_table", "limma", "statmod"] 9707 }, 9708 "limpca": { 9709 "name": "limpca", 9710 "version": "1.6.0", 9711 "sha256": "0820zpw7p18dha8bypvmxck5c8wqjjm0s9l1wycn01g6jidkxizl", 9712 "depends": ["S4Vectors", "SummarizedExperiment", "doParallel", "dplyr", "ggplot2", "ggrepel", "ggsci", "plyr", "reshape2", "stringr", "tibble", "tidyr", "tidyverse"] 9713 }, 9714 "lineagespot": { 9715 "name": "lineagespot", 9716 "version": "1.14.0", 9717 "sha256": "1m0xc2i611py0q5293jp998z7x3bznfzx3p30fylv7sr5vwa98xb", 9718 "depends": ["MatrixGenerics", "SummarizedExperiment", "VariantAnnotation", "data_table", "httr", "stringr"] 9719 }, 9720 "linkSet": { 9721 "name": "linkSet", 9722 "version": "1.0.0", 9723 "sha256": "1rsivkr48fpspqh4771i7irl1n0bpaaf3nkm82gr9pxp293rhgz3", 9724 "depends": ["AnnotationDbi", "BiocGenerics", "DBI", "GenomeInfoDb", "GenomicRanges", "IRanges", "InteractionSet", "MASS", "Organism_dplyr", "S4Vectors", "data_table", "doParallel", "foreach", "ggplot2", "iterators", "patchwork", "rlang", "scales"] 9725 }, 9726 "lionessR": { 9727 "name": "lionessR", 9728 "version": "1.24.0", 9729 "sha256": "077j3fh2i2ikkpaaxkf9y1cc4kbii83x0b7fxnpps69d018hc9fp", 9730 "depends": ["S4Vectors", "SummarizedExperiment"] 9731 }, 9732 "lipidr": { 9733 "name": "lipidr", 9734 "version": "2.24.0", 9735 "sha256": "1hjwglxngn4b3xss702cpfq05q27bk6jkg7sdxhpcxj07976mpgw", 9736 "depends": ["S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "fgsea", "forcats", "ggplot2", "imputeLCMD", "limma", "magrittr", "rlang", "ropls", "tidyr"] 9737 }, 9738 "lisaClust": { 9739 "name": "lisaClust", 9740 "version": "1.18.0", 9741 "sha256": "1c3zx3s3mv980gy9s2n7763q5sas552msvgx8x4dmik569g6kv08", 9742 "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "class", "concaveman", "data_table", "dplyr", "ggplot2", "lifecycle", "pheatmap", "purrr", "rlang", "simpleSeg", "spatstat_explore", "spatstat_geom", "spatstat_random", "spicyR", "tidyr"] 9743 }, 9744 "lmdme": { 9745 "name": "lmdme", 9746 "version": "1.52.0", 9747 "sha256": "15a9wzz3rhwdvv8wvpfm8v2c4casa9qj0m162hrz6dnc07mwxnnj", 9748 "depends": ["limma", "pls", "stemHypoxia"] 9749 }, 9750 "loci2path": { 9751 "name": "loci2path", 9752 "version": "1.30.0", 9753 "sha256": "1384sfssk8xv28g7vjib3qjswq58cqnzwnlxyrj1yasj7aid2r0n", 9754 "depends": ["BiocParallel", "GenomicRanges", "RColorBrewer", "S4Vectors", "data_table", "pheatmap", "wordcloud"] 9755 }, 9756 "logicFS": { 9757 "name": "logicFS", 9758 "version": "2.30.0", 9759 "sha256": "0bg85d0kmzwyviywmrwvdn6qczajqzbzzzkwfawzgmp5p65ssgfk", 9760 "depends": ["LogicReg", "mcbiopi", "survival"] 9761 }, 9762 "looking4clusters": { 9763 "name": "looking4clusters", 9764 "version": "1.0.0", 9765 "sha256": "1982qhk0zj9q7wxzd3qflwcv71z8bz3f3zn4yc72zqpdx7hf80z8", 9766 "depends": ["BiocBaseUtils", "SingleCellExperiment", "SummarizedExperiment", "jsonlite"] 9767 }, 9768 "lpNet": { 9769 "name": "lpNet", 9770 "version": "2.42.0", 9771 "sha256": "027d9iiqrxfmr86hnvnfc3g5bk23qnly05xz0akxx1yrvmka369q", 9772 "depends": ["KEGGgraph", "lpSolve"] 9773 }, 9774 "lpsymphony": { 9775 "name": "lpsymphony", 9776 "version": "1.38.0", 9777 "sha256": "0l3zf7f9agkwcm4xbnws7ld77w7fiqx26qjh5rzyvvzprb65xiax", 9778 "depends": [] 9779 }, 9780 "lumi": { 9781 "name": "lumi", 9782 "version": "2.62.0", 9783 "sha256": "0m20f9399wdf778kgmgdf5fc4axbbq8shynrwjraa0smlr5zg6zy", 9784 "depends": ["AnnotationDbi", "Biobase", "DBI", "GenomicFeatures", "GenomicRanges", "KernSmooth", "MASS", "RSQLite", "affy", "annotate", "lattice", "methylumi", "mgcv", "nleqslv", "preprocessCore"] 9785 }, 9786 "m6Aboost": { 9787 "name": "m6Aboost", 9788 "version": "1.16.0", 9789 "sha256": "0vldnbc56w2mv7c994lwydgh5ij3bi85ws7pa1dqvn1fkvyf7r0v", 9790 "depends": ["BSgenome", "Biostrings", "ExperimentHub", "GenomicRanges", "IRanges", "S4Vectors", "adabag", "dplyr", "rtracklayer"] 9791 }, 9792 "mBPCR": { 9793 "name": "mBPCR", 9794 "version": "1.64.0", 9795 "sha256": "0xl7si4d3r3akfqym9v2kxrsji1gzdm6wlyan1lclqjdb3qlwai9", 9796 "depends": ["Biobase", "GWASTools", "oligoClasses"] 9797 }, 9798 "maCorrPlot": { 9799 "name": "maCorrPlot", 9800 "version": "1.80.0", 9801 "sha256": "0yppp6dcrnxfi3kb37x8zkkhz93bm84svfpbs39v5q1h5qcrn7kn", 9802 "depends": ["lattice"] 9803 }, 9804 "maPredictDSC": { 9805 "name": "maPredictDSC", 9806 "version": "1.48.0", 9807 "sha256": "1kqxwqpm82457bjswmgkc3ycda0j7fnknaa74v5ghl7lsp267np0", 9808 "depends": ["AnnotationDbi", "LungCancerACvsSCCGEO", "MASS", "ROC", "ROCR", "affy", "caret", "class", "e1071", "gcrma", "hgu133plus2_db", "limma"] 9809 }, 9810 "maSigPro": { 9811 "name": "maSigPro", 9812 "version": "1.82.0", 9813 "sha256": "13l7nasczy4nyqwyrvcw3ki575phjz7rcc4127qvkx0cbxkvmkha", 9814 "depends": ["Biobase", "MASS", "mclust", "venn"] 9815 }, 9816 "maaslin3": { 9817 "name": "maaslin3", 9818 "version": "1.2.0", 9819 "sha256": "0dlr8k9h6m95six3sbinczrvf9778qba0bf1gng51062zhw0hkdc", 9820 "depends": ["BiocGenerics", "RColorBrewer", "SummarizedExperiment", "TreeSummarizedExperiment", "dplyr", "ggnewscale", "ggplot2", "lme4", "lmerTest", "logging", "multcomp", "optparse", "patchwork", "pbapply", "plyr", "rlang", "scales", "survival", "tibble"] 9821 }, 9822 "made4": { 9823 "name": "made4", 9824 "version": "1.84.0", 9825 "sha256": "16lcqxwafjmsslydxn6jd4jyvapbky8alsqdnc7bh3lmlmz3kv8v", 9826 "depends": ["Biobase", "RColorBrewer", "SummarizedExperiment", "ade4", "gplots", "scatterplot3d"] 9827 }, 9828 "maftools": { 9829 "name": "maftools", 9830 "version": "2.26.0", 9831 "sha256": "0s9a119rrk0l4p8vq6bbg2b9m465ihkdhxiv64my77a4f93i31n1", 9832 "depends": ["DNAcopy", "RColorBrewer", "Rhtslib", "data_table", "pheatmap", "survival"] 9833 }, 9834 "magpie": { 9835 "name": "magpie", 9836 "version": "1.10.0", 9837 "sha256": "1vcv4xn55x8m08f8krrpn1ap22f9247gs7817p8bqm58lxlj9r05", 9838 "depends": ["AnnotationDbi", "BiocParallel", "DESeq2", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "Rsamtools", "S4Vectors", "TRESS", "aod", "matrixStats", "openxlsx", "reshape2", "rtracklayer"] 9839 }, 9840 "magrene": { 9841 "name": "magrene", 9842 "version": "1.12.0", 9843 "sha256": "0fn60g28m839kmrnvdzh6ywgi72d4yww0z824i1v9z6v7hjjmn0d", 9844 "depends": ["BiocParallel"] 9845 }, 9846 "makecdfenv": { 9847 "name": "makecdfenv", 9848 "version": "1.86.0", 9849 "sha256": "1sxx9986nv9bpwxp3gpxfbk7vagqig914cds12bfvjyfxwg49wfz", 9850 "depends": ["Biobase", "affy", "affyio"] 9851 }, 9852 "mapscape": { 9853 "name": "mapscape", 9854 "version": "1.34.0", 9855 "sha256": "1rx81aasdi1hg2a3ywqczjgnwrz1axdfkpn91yz2qrj9v7d6zcdi", 9856 "depends": ["base64enc", "htmlwidgets", "jsonlite", "stringr"] 9857 }, 9858 "mariner": { 9859 "name": "mariner", 9860 "version": "1.10.0", 9861 "sha256": "0i2y0q4icmbj7z7hb1qjrhxj7lg0k3l2fl03125z0hi0d8pb0qfq", 9862 "depends": ["BiocGenerics", "BiocManager", "BiocParallel", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "InteractionSet", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "abind", "assertthat", "colourvalues", "data_table", "dbscan", "glue", "magrittr", "plotgardener", "plyranges", "progress", "purrr", "rhdf5", "rlang", "strawr"] 9863 }, 9864 "markeR": { 9865 "name": "markeR", 9866 "version": "1.0.0", 9867 "sha256": "1k51rp13y8cq0p0kxsbzcvz1dmarw02ifvf784nq2d1a1v7qzda2", 9868 "depends": ["ComplexHeatmap", "RColorBrewer", "circlize", "edgeR", "effectsize", "fgsea", "ggh4x", "ggplot2", "ggpubr", "ggrepel", "gridExtra", "limma", "msigdbr", "pROC", "reshape2", "rstatix", "scales", "tibble"] 9869 }, 9870 "marr": { 9871 "name": "marr", 9872 "version": "1.20.0", 9873 "sha256": "1q89n1pzzf5w742aqgcygcid0dnx8vn8z1ygkl1q9ldpdyanpmg0", 9874 "depends": ["Rcpp", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "magrittr", "rlang"] 9875 }, 9876 "marray": { 9877 "name": "marray", 9878 "version": "1.88.0", 9879 "sha256": "01zv8fx8yf1i8zk3mbfzygm3ys8gfrbfir8bbki08n8zk8bxj1r8", 9880 "depends": ["limma"] 9881 }, 9882 "martini": { 9883 "name": "martini", 9884 "version": "1.30.0", 9885 "sha256": "1j44n3qi1gls2dn8zhx8p8k18z95bqnmi6a88divl2xlxv9q520q", 9886 "depends": ["Matrix", "Rcpp", "RcppEigen", "igraph", "memoise", "snpStats"] 9887 }, 9888 "maser": { 9889 "name": "maser", 9890 "version": "1.28.0", 9891 "sha256": "0h41vajx7dvacp62bl8fab9zmv6fhnzjwdprvh0lrg26j7zivk9i", 9892 "depends": ["BiocGenerics", "DT", "GenomicRanges", "Gviz", "IRanges", "Seqinfo", "data_table", "dplyr", "ggplot2", "reshape2", "rtracklayer"] 9893 }, 9894 "maskBAD": { 9895 "name": "maskBAD", 9896 "version": "1.54.0", 9897 "sha256": "0fcbj4v8k5na9iina6458ngk79mq3q147g6x5yj3k65gyy6ik0i7", 9898 "depends": ["affy", "gcrma"] 9899 }, 9900 "massiR": { 9901 "name": "massiR", 9902 "version": "1.46.0", 9903 "sha256": "0dgzld48idxxfxghq4q4c8gpn6szhg7l54cm349jp5wwi7fwk6gq", 9904 "depends": ["Biobase", "cluster", "diptest", "gplots"] 9905 }, 9906 "mastR": { 9907 "name": "mastR", 9908 "version": "1.10.0", 9909 "sha256": "1pdy3yzlkvf1j3j1zi8w1jy1rllacrp228i5wi57r8d32cp8y283", 9910 "depends": ["AnnotationDbi", "Biobase", "GSEABase", "Matrix", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "edgeR", "ggplot2", "ggpubr", "limma", "msigdb", "org_Hs_eg_db", "patchwork", "tidyr"] 9911 }, 9912 "matchBox": { 9913 "name": "matchBox", 9914 "version": "1.52.0", 9915 "sha256": "11gsigii003rjcqpp2ia85pwwpf36j8q6wr1w94ya7874gxcrkgq", 9916 "depends": [] 9917 }, 9918 "matter": { 9919 "name": "matter", 9920 "version": "2.12.0", 9921 "sha256": "0r8jpxx3zr498fj890l34rwidmq3zgyq289f7dblfkz70ma6j47i", 9922 "depends": ["BH", "BiocGenerics", "BiocParallel", "Matrix", "ProtGenerics", "digest", "irlba"] 9923 }, 9924 "mbQTL": { 9925 "name": "mbQTL", 9926 "version": "1.10.0", 9927 "sha256": "0mbi87d12yjfdbrplc4906i6hm7nifsy7ar3wi8fgwjs220r38df", 9928 "depends": ["MatrixEQTL", "broom", "dplyr", "ggplot2", "metagenomeSeq", "pheatmap", "readxl", "stringr", "tidyr"] 9929 }, 9930 "mbkmeans": { 9931 "name": "mbkmeans", 9932 "version": "1.26.0", 9933 "sha256": "1sa10gnc962311c7hgmjb3c51hz7s3704yfs2bf7kxzfjyja402s", 9934 "depends": ["BiocParallel", "ClusterR", "DelayedArray", "Matrix", "Rcpp", "RcppArmadillo", "Rhdf5lib", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "beachmat", "benchmarkme"] 9935 }, 9936 "mdp": { 9937 "name": "mdp", 9938 "version": "1.30.0", 9939 "sha256": "1r0m5700kqnq9g0lbsgk6iv96vkriwqlk6k2jk5igdlhww75hkwq", 9940 "depends": ["ggplot2", "gridExtra"] 9941 }, 9942 "mdqc": { 9943 "name": "mdqc", 9944 "version": "1.72.0", 9945 "sha256": "1cifi9zhy1fv733b39crznkj2kjxxh34aygdvzz1gk7g8b7zcs5j", 9946 "depends": ["MASS", "cluster"] 9947 }, 9948 "megadepth": { 9949 "name": "megadepth", 9950 "version": "1.20.0", 9951 "sha256": "115zxqa0dbamc4p6kx9zxc06y0agz7dmi059afw4ci2qyx73smsp", 9952 "depends": ["GenomicRanges", "cmdfun", "dplyr", "fs", "magrittr", "readr", "xfun"] 9953 }, 9954 "memes": { 9955 "name": "memes", 9956 "version": "1.18.0", 9957 "sha256": "14gwcrpxwgz0amgm25l00x129kln3fd40if2r1qgvbmlff1cx9sq", 9958 "depends": ["Biostrings", "GenomicRanges", "cmdfun", "dplyr", "ggplot2", "ggseqlogo", "magrittr", "matrixStats", "patchwork", "processx", "purrr", "readr", "rlang", "tibble", "tidyr", "universalmotif", "usethis", "xml2"] 9959 }, 9960 "meshes": { 9961 "name": "meshes", 9962 "version": "1.36.0", 9963 "sha256": "01mm15crzsg6z7j5ww93ig557j272vk9bgfihbgvi4da8zmasv8c", 9964 "depends": ["AnnotationDbi", "AnnotationHub", "DOSE", "GOSemSim", "MeSHDbi", "enrichplot", "yulab_utils"] 9965 }, 9966 "meshr": { 9967 "name": "meshr", 9968 "version": "2.16.0", 9969 "sha256": "0lqj3yh2kyapjvbgh8w1bwdj96dhzxxs3zyqz2r6his0b28kdjfr", 9970 "depends": ["BiocGenerics", "BiocStyle", "Category", "MeSHDbi", "RSQLite", "S4Vectors", "fdrtool", "knitr", "markdown", "rmarkdown"] 9971 }, 9972 "messina": { 9973 "name": "messina", 9974 "version": "1.46.0", 9975 "sha256": "0n1jjiqhpgrnbs7nnp0sf281xlz1i0rxk2957fdlwa8f602akg3y", 9976 "depends": ["Rcpp", "foreach", "ggplot2", "plyr", "survival"] 9977 }, 9978 "metaCCA": { 9979 "name": "metaCCA", 9980 "version": "1.38.0", 9981 "sha256": "1jzh9qr66wzrnz5c5xsv9y414nm62ziph2ldcd8fachvqc7wwnls", 9982 "depends": [] 9983 }, 9984 "metaMS": { 9985 "name": "metaMS", 9986 "version": "1.46.0", 9987 "sha256": "0cymdlv8sjamcs82k3xcjykhfin5fqyyamz8xwrj19pxa2hfr7x9", 9988 "depends": ["BiocGenerics", "CAMERA", "Matrix", "robustbase", "xcms"] 9989 }, 9990 "metaSeq": { 9991 "name": "metaSeq", 9992 "version": "1.50.0", 9993 "sha256": "1jz4fyspc7pvrddm40xp79d3bh0agiqx68sp4i2y3cbrzba2y5xq", 9994 "depends": ["NOISeq", "Rcpp", "snow"] 9995 }, 9996 "metabCombiner": { 9997 "name": "metabCombiner", 9998 "version": "1.20.0", 9999 "sha256": "1v771vqpjpxx7yng1hnci7nrxqbxzv3ns471r1nl1svjghngklmm", 10000 "depends": ["S4Vectors", "caret", "dplyr", "matrixStats", "mgcv", "rlang", "tidyr"] 10001 }, 10002 "metabinR": { 10003 "name": "metabinR", 10004 "version": "1.12.0", 10005 "sha256": "0pda023fw6qbybp68p9mmcxr9slf24fsqf9agsn4b9207pmr20pp", 10006 "depends": ["rJava"] 10007 }, 10008 "metabomxtr": { 10009 "name": "metabomxtr", 10010 "version": "1.44.0", 10011 "sha256": "1rmxjnx22kr08ppazpsjb5nmq0ji4wj73kmxn0pd5ixivwkz1bin", 10012 "depends": ["Biobase", "BiocParallel", "Formula", "ggplot2", "multtest", "optimx", "plyr"] 10013 }, 10014 "metagene2": { 10015 "name": "metagene2", 10016 "version": "1.26.0", 10017 "sha256": "0a9kmm66qpgf1n8jj7h0c05h2vdkg7kw9lc190dyv9hk6fy542m1", 10018 "depends": ["BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "R6", "Rsamtools", "data_table", "dplyr", "ggplot2", "magrittr", "purrr", "reshape2", "rtracklayer"] 10019 }, 10020 "metagenomeSeq": { 10021 "name": "metagenomeSeq", 10022 "version": "1.52.0", 10023 "sha256": "0bkgf6kyh7j767cynxcxqm9xxrqxfq0zzps82hj168n27agx5m30", 10024 "depends": ["Biobase", "Matrix", "RColorBrewer", "Wrench", "foreach", "glmnet", "gplots", "limma", "matrixStats"] 10025 }, 10026 "metahdep": { 10027 "name": "metahdep", 10028 "version": "1.68.0", 10029 "sha256": "09rxii0nsrckkr383192sn926s45zc5wpds9rv04fz4f47m1s2qy", 10030 "depends": [] 10031 }, 10032 "metapod": { 10033 "name": "metapod", 10034 "version": "1.18.0", 10035 "sha256": "1wfy183k5zk41yjr6wlp8jzhjjz2bkqjdifmz1w6fky25ry700gi", 10036 "depends": ["Rcpp"] 10037 }, 10038 "metapone": { 10039 "name": "metapone", 10040 "version": "1.16.0", 10041 "sha256": "13bblag8w907qddcvbaqjvlqpbyj23c5jb1cghkajqpf1pn3gmdl", 10042 "depends": ["BiocParallel", "fdrtool", "fgsea", "fields", "ggplot2", "ggrepel", "markdown"] 10043 }, 10044 "metaseqR2": { 10045 "name": "metaseqR2", 10046 "version": "1.22.0", 10047 "sha256": "01s9gpndc1skpq69wdsm1kgcz7n4i1zm38g731zphhnw4w3kad54", 10048 "depends": ["ABSSeq", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DESeq2", "DSS", "DT", "EDASeq", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "Matrix", "NBPSeq", "RSQLite", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VennDiagram", "biomaRt", "corrplot", "edgeR", "genefilter", "gplots", "harmonicmeanp", "heatmaply", "htmltools", "httr", "jsonlite", "lattice", "limma", "locfit", "log4r", "magrittr", "pander", "qvalue", "rmarkdown", "rmdformats", "rtracklayer", "stringr", "survcomp", "txdbmaker", "vsn", "yaml", "zoo"] 10049 }, 10050 "methInheritSim": { 10051 "name": "methInheritSim", 10052 "version": "1.32.0", 10053 "sha256": "1j53b5d3wfkj0i84sq0aj6nx9adiavjg64bh0xwaq78n7qn6sbm6", 10054 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "methylKit", "msm"] 10055 }, 10056 "methimpute": { 10057 "name": "methimpute", 10058 "version": "1.32.0", 10059 "sha256": "0zl945lhl291fsbdwgdyqlc3fy8i7z4bn2a21p2j0ald11s63x6d", 10060 "depends": ["Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rcpp", "data_table", "ggplot2", "minpack_lm", "reshape2"] 10061 }, 10062 "methodical": { 10063 "name": "methodical", 10064 "version": "1.6.0", 10065 "sha256": "14mrc00ya5a372j5q2rrxxp54cbwridaz2b5mm45wqvwgms6bvg5", 10066 "depends": ["AnnotationHub", "BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BiocCheck", "BiocManager", "BiocParallel", "BiocStyle", "Biostrings", "DelayedArray", "ExperimentHub", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "MatrixGenerics", "R_utils", "RcppRoll", "S4Vectors", "SummarizedExperiment", "TumourMethData", "annotatr", "cowplot", "data_table", "devtools", "dplyr", "foreach", "ggplot2", "knitr", "rcmdcheck", "remotes", "rhdf5", "rtracklayer", "scales", "tibble", "tidyr", "usethis"] 10067 }, 10068 "methrix": { 10069 "name": "methrix", 10070 "version": "1.24.0", 10071 "sha256": "1jlbk6yb9815xrgar9nc8g8qzl93451gcx6smr7s2agzxnpxi8vz", 10072 "depends": ["BSgenome", "DelayedArray", "DelayedMatrixStats", "GenomicRanges", "HDF5Array", "IRanges", "S4Vectors", "SummarizedExperiment", "data_table", "ggplot2", "matrixStats", "rtracklayer"] 10073 }, 10074 "methyLImp2": { 10075 "name": "methyLImp2", 10076 "version": "1.6.0", 10077 "sha256": "1800chr3r65iqpdjxymqd6sjg81ckvv841ycdad1xrpva9g6dv8g", 10078 "depends": ["BiocParallel", "ChAMPdata", "SummarizedExperiment", "corpcor"] 10079 }, 10080 "methylCC": { 10081 "name": "methylCC", 10082 "version": "1.24.0", 10083 "sha256": "1m4n82knw39yzlnir7v3ddkfgl66nxgcafsn4sd7a7kldvh9kzwc", 10084 "depends": ["Biobase", "FlowSorted_Blood_450k", "GenomicRanges", "IRanges", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "S4Vectors", "bsseq", "bumphunter", "dplyr", "genefilter", "magrittr", "minfi", "plyranges", "quadprog"] 10085 }, 10086 "methylGSA": { 10087 "name": "methylGSA", 10088 "version": "1.28.0", 10089 "sha256": "0980n655ahjadi3d052x5mf7w6n9m79ly9188if9d9dqq9ggmncn", 10090 "depends": ["AnnotationDbi", "BiocParallel", "GO_db", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylationEPICanno_ilm10b4_hg19", "RobustRankAggreg", "clusterProfiler", "ggplot2", "missMethyl", "org_Hs_eg_db", "reactome_db", "shiny", "stringr"] 10091 }, 10092 "methylInheritance": { 10093 "name": "methylInheritance", 10094 "version": "1.34.0", 10095 "sha256": "1b6i1szvzh9bc4hryq8czmz7c5l70aqc8i2lrzhf40sga7iahg6q", 10096 "depends": ["BiocParallel", "GenomicRanges", "IRanges", "S4Vectors", "ggplot2", "gridExtra", "methylKit", "rebus"] 10097 }, 10098 "methylKit": { 10099 "name": "methylKit", 10100 "version": "1.36.0", 10101 "sha256": "0ay3x7scmp7j3g3vqlyb3w2cnakaw2bbprj7fsdy6mda7py9p2qi", 10102 "depends": ["GenomicRanges", "IRanges", "KernSmooth", "R_utils", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "Seqinfo", "data_table", "emdbook", "fastseg", "gtools", "limma", "mclust", "mgcv", "qvalue", "rtracklayer"] 10103 }, 10104 "methylMnM": { 10105 "name": "methylMnM", 10106 "version": "1.48.0", 10107 "sha256": "0h946n923mqmcbvbs2lrxh9wdnwhxg7nmbhhq0nd1na480bqa6cb", 10108 "depends": ["edgeR", "statmod"] 10109 }, 10110 "methylPipe": { 10111 "name": "methylPipe", 10112 "version": "1.44.0", 10113 "sha256": "1lzkpc54j4idw1zcfj7cbjq42in25f4nk8cvkif5w0a6z0h4djjn", 10114 "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "GenomicRanges", "Gviz", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "data_table", "gplots", "marray"] 10115 }, 10116 "methylSig": { 10117 "name": "methylSig", 10118 "version": "1.22.0", 10119 "sha256": "155dky5z1gdrkns96hr8vvrickidwsjzk5z0c75rkfnqhk8dqjg6", 10120 "depends": ["DSS", "DelayedArray", "DelayedMatrixStats", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "bsseq"] 10121 }, 10122 "methylclock": { 10123 "name": "methylclock", 10124 "version": "1.16.0", 10125 "sha256": "0kxdygwna7qxnk6v29aj8b5n43vhag61sjkd761vy76ngxvs202c", 10126 "depends": ["Biobase", "ExperimentHub", "PerformanceAnalytics", "RPMM", "Rcpp", "devtools", "dplyr", "dynamicTreeCut", "ggplot2", "ggpmisc", "ggpubr", "gridExtra", "impute", "methylclockData", "minfi", "planet", "preprocessCore", "quadprog", "tibble", "tidyr", "tidyverse"] 10127 }, 10128 "methylscaper": { 10129 "name": "methylscaper", 10130 "version": "1.18.0", 10131 "sha256": "1g2h09ivqrgm52dv5nr2pbrwk94h58s9f7inc0wilj8miv9iby91", 10132 "depends": ["BiocParallel", "Biostrings", "Rfast", "SummarizedExperiment", "data_table", "pwalign", "seqinr", "seriation", "shiny", "shinyFiles", "shinyjs"] 10133 }, 10134 "methylumi": { 10135 "name": "methylumi", 10136 "version": "2.56.0", 10137 "sha256": "0wxyy8wiz85x3ls29gm3s64p1vqhfi3av1j6zzm8xwxi8fjlnv1y", 10138 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "FDb_InfiniumMethylation_hg19", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "annotate", "genefilter", "ggplot2", "illuminaio", "lattice", "matrixStats", "minfi", "reshape2", "scales"] 10139 }, 10140 "mgsa": { 10141 "name": "mgsa", 10142 "version": "1.58.0", 10143 "sha256": "0cfhqjf86p9c00c1nn0yy9zqgqxs3v8wikp1k3jidpd1fq6g778n", 10144 "depends": ["gplots"] 10145 }, 10146 "miQC": { 10147 "name": "miQC", 10148 "version": "1.18.0", 10149 "sha256": "1iw726i35icmzx7qjlh4gddng96h6yrzg6iy8pqi64ys4i1fvirb", 10150 "depends": ["SingleCellExperiment", "flexmix", "ggplot2"] 10151 }, 10152 "miRBaseConverter": { 10153 "name": "miRBaseConverter", 10154 "version": "1.34.0", 10155 "sha256": "09710mz03lnvh45969nbzwdfl699yzmf745kwm8yzkl2djgipb6q", 10156 "depends": [] 10157 }, 10158 "miRLAB": { 10159 "name": "miRLAB", 10160 "version": "1.40.0", 10161 "sha256": "17sg5y6xk3szvjcn5cd2jq3n5p47df0hckk9pdzsc2ac7z7vvljr", 10162 "depends": ["Category", "GOstats", "Hmisc", "InvariantCausalPrediction", "RCurl", "SummarizedExperiment", "TCGAbiolinks", "ctc", "dplyr", "energy", "entropy", "glmnet", "gplots", "httr", "impute", "limma", "org_Hs_eg_db", "pcalg", "stringr"] 10163 }, 10164 "miRNAmeConverter": { 10165 "name": "miRNAmeConverter", 10166 "version": "1.38.0", 10167 "sha256": "025590pfljckxp2bvb83g974sxi8zprbhgixkcglb5szxpvsr1j5", 10168 "depends": ["AnnotationDbi", "DBI", "miRBaseVersions_db", "reshape2"] 10169 }, 10170 "miRNApath": { 10171 "name": "miRNApath", 10172 "version": "1.70.0", 10173 "sha256": "09jdm41iqg9ivka8ypyqjfqd7rpm7g5llwk4y9r7jykhjwh2j6d0", 10174 "depends": [] 10175 }, 10176 "miRNAtap": { 10177 "name": "miRNAtap", 10178 "version": "1.44.0", 10179 "sha256": "13grr33knsgimxb74nmsjahih33zxcq2i2b1ghzxz47c2pc7k721", 10180 "depends": ["AnnotationDbi", "DBI", "RSQLite", "plyr", "sqldf", "stringr"] 10181 }, 10182 "miRSM": { 10183 "name": "miRSM", 10184 "version": "2.6.0", 10185 "sha256": "1643mfcfa7a8zmn4pkrgxvr4qhzqwxh91rg8ww17vcqgli3imvf1", 10186 "depends": ["BiBitR", "BicARE", "Biobase", "DOSE", "GFA", "GSEABase", "MCL", "MatrixCorrelation", "NMF", "PMA", "RColorBrewer", "Rcpp", "ReactomePA", "SOMbrero", "SummarizedExperiment", "WGCNA", "biclust", "clusterProfiler", "dbscan", "dynamicTreeCut", "energy", "fabia", "flashClust", "iBBiG", "igraph", "isa2", "mclust", "org_Hs_eg_db", "ppclust", "rJava", "rqubic"] 10187 }, 10188 "miRcomp": { 10189 "name": "miRcomp", 10190 "version": "1.40.0", 10191 "sha256": "0g2s82wzvd2zlzlgscwmyi918brklrjhb9b2fljxr8rc25hiy8sm", 10192 "depends": ["Biobase", "KernSmooth", "miRcompData"] 10193 }, 10194 "miRspongeR": { 10195 "name": "miRspongeR", 10196 "version": "2.14.0", 10197 "sha256": "0mgfff2kiblr60ymdj31j856lgrai2chlcc54vsmz88pljsb605q", 10198 "depends": ["DOSE", "MCL", "RColorBrewer", "Rcpp", "ReactomePA", "SPONGE", "clusterProfiler", "corpcor", "doParallel", "foreach", "igraph", "org_Hs_eg_db", "survival"] 10199 }, 10200 "mia": { 10201 "name": "mia", 10202 "version": "1.18.0", 10203 "sha256": "0rn8y72mlyqk1ss52phg02sj1j6159la8b86hjc83cavrwy9gczn", 10204 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "DECIPHER", "DelayedArray", "DelayedMatrixStats", "DirichletMultinomial", "IRanges", "MASS", "MatrixGenerics", "MultiAssayExperiment", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "bluster", "decontam", "dplyr", "rbiom", "rlang", "scater", "scuttle", "stringr", "tibble", "tidyr", "vegan"] 10205 }, 10206 "miaDash": { 10207 "name": "miaDash", 10208 "version": "1.2.0", 10209 "sha256": "0xjb277vl403f968f2lxasp6xvid7iai6wgng67q6c0a4y5fhzli", 10210 "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "bluster", "htmltools", "iSEE", "iSEEtree", "mia", "rintrojs", "scater", "scuttle", "shiny", "shinyWidgets", "shinydashboard", "shinyjs", "vegan"] 10211 }, 10212 "miaSim": { 10213 "name": "miaSim", 10214 "version": "1.16.0", 10215 "sha256": "0smnz25wq9vjpf7a86awfwp519ivc44d91ifj85g20priv6aj65m", 10216 "depends": ["MatrixGenerics", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "deSolve", "poweRlaw"] 10217 }, 10218 "miaTime": { 10219 "name": "miaTime", 10220 "version": "1.0.0", 10221 "sha256": "1glkmlf7vcbvvn9zscq79npcysyws2rj6ww70sbgpl98jbfnla4b", 10222 "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "dplyr", "mia", "tidyr"] 10223 }, 10224 "miaViz": { 10225 "name": "miaViz", 10226 "version": "1.18.0", 10227 "sha256": "1zqicbb6bmx9whw0knmbf2z9ghypyrqf0rcjfvayfjb5gk404aba", 10228 "depends": ["BiocGenerics", "BiocParallel", "DelayedArray", "DirichletMultinomial", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "dplyr", "ggnewscale", "ggplot2", "ggraph", "ggrepel", "ggtree", "mia", "rlang", "scales", "scater", "tibble", "tidygraph", "tidyr", "tidytext", "tidytree", "viridis"] 10229 }, 10230 "microRNA": { 10231 "name": "microRNA", 10232 "version": "1.68.0", 10233 "sha256": "0bwgqbxqx4y84vazc9fa5p3jpys8wyq24wcs82rlha72y9527f9i", 10234 "depends": ["Biostrings"] 10235 }, 10236 "microbiome": { 10237 "name": "microbiome", 10238 "version": "1.32.0", 10239 "sha256": "155sap719s2p52kqlkgjfgaazk4c376fq2y0055zbjfxn688z9bb", 10240 "depends": ["Biostrings", "Rtsne", "compositions", "dplyr", "ggplot2", "phyloseq", "reshape2", "scales", "tibble", "tidyr", "vegan"] 10241 }, 10242 "microbiomeDASim": { 10243 "name": "microbiomeDASim", 10244 "version": "1.24.0", 10245 "sha256": "1gwn93vd73fi8d2kgqkznc2gi52hywja7jdnzw8l16w4m5isjh2n", 10246 "depends": ["Biobase", "MASS", "Matrix", "ggplot2", "metagenomeSeq", "mvtnorm", "pbapply", "phyloseq", "tmvtnorm"] 10247 }, 10248 "microbiomeExplorer": { 10249 "name": "microbiomeExplorer", 10250 "version": "1.20.0", 10251 "sha256": "0kjbady0qdavjszs1vcb9gmri885mick26ml8426y513ng15h95c", 10252 "depends": ["Biobase", "DESeq2", "DT", "RColorBrewer", "biomformat", "broom", "car", "dplyr", "forcats", "heatmaply", "knitr", "limma", "lubridate", "magrittr", "matrixStats", "metagenomeSeq", "plotly", "purrr", "readr", "reshape2", "rlang", "rmarkdown", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinyjs", "stringr", "tibble", "tidyr", "vegan"] 10253 }, 10254 "midasHLA": { 10255 "name": "midasHLA", 10256 "version": "1.18.0", 10257 "sha256": "1naxs3khgnz937n7kjfszpryjfj0ymrrl1nyikz07myrkzn0cxam", 10258 "depends": ["HardyWeinberg", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "assertthat", "broom", "dplyr", "formattable", "kableExtra", "knitr", "magrittr", "qdapTools", "rlang", "stringi", "tibble"] 10259 }, 10260 "miloR": { 10261 "name": "miloR", 10262 "version": "2.6.0", 10263 "sha256": "10m82jnhfzv2jkknjy7y4mha5cvr4k2m0rs58yb12505aw9n9lda", 10264 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "Matrix", "MatrixGenerics", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppML", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cowplot", "dplyr", "edgeR", "ggbeeswarm", "ggplot2", "ggraph", "ggrepel", "gtools", "igraph", "irlba", "limma", "matrixStats", "numDeriv", "patchwork", "pracma", "stringr", "tibble", "tidyr"] 10265 }, 10266 "mimager": { 10267 "name": "mimager", 10268 "version": "1.34.0", 10269 "sha256": "081gpygmy0m9pgggznpcq2dw209vx76ip8ayyn9as699fpqiy1ks", 10270 "depends": ["Biobase", "BiocGenerics", "DBI", "S4Vectors", "affy", "affyPLM", "gtable", "oligo", "oligoClasses", "preprocessCore", "scales"] 10271 }, 10272 "mina": { 10273 "name": "mina", 10274 "version": "1.18.0", 10275 "sha256": "1pqjir3f8r8rmhg78agccvc0yqwch1nyyanpps6r6d2qlhb5xd16", 10276 "depends": ["Hmisc", "MCL", "RSpectra", "Rcpp", "RcppArmadillo", "RcppParallel", "apcluster", "biganalytics", "bigmemory", "foreach", "ggplot2", "parallelDist", "plyr", "reshape2", "stringr"] 10277 }, 10278 "minet": { 10279 "name": "minet", 10280 "version": "3.68.0", 10281 "sha256": "0i1sr5yyn3vwqs5m48z92xcw8ihx21r5r2y0ggqc16a0j5r5rm4g", 10282 "depends": ["infotheo"] 10283 }, 10284 "minfi": { 10285 "name": "minfi", 10286 "version": "1.56.0", 10287 "sha256": "1rnaiy8m2nklrn9plf1ca6w0d755iib737s9zmllacrz8lc6b1ik", 10288 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "DelayedArray", "DelayedMatrixStats", "GEOquery", "GenomicRanges", "HDF5Array", "IRanges", "MASS", "RColorBrewer", "S4Vectors", "Seqinfo", "SummarizedExperiment", "beanplot", "bumphunter", "data_table", "genefilter", "illuminaio", "lattice", "limma", "mclust", "nlme", "nor1mix", "preprocessCore", "quadprog", "reshape", "siggenes"] 10289 }, 10290 "mirIntegrator": { 10291 "name": "mirIntegrator", 10292 "version": "1.40.0", 10293 "sha256": "0y8xqjcfmz7f89501vmm4n94p88z61ibdz8jn1gl2csnp2i6p781", 10294 "depends": ["AnnotationDbi", "ROntoTools", "Rgraphviz", "ggplot2", "graph", "org_Hs_eg_db"] 10295 }, 10296 "mirTarRnaSeq": { 10297 "name": "mirTarRnaSeq", 10298 "version": "1.18.0", 10299 "sha256": "0569hc22mmpaaiyh799ijfhi7zfq45vif25cy8wgk2zfvd73fhza", 10300 "depends": ["MASS", "R_utils", "assertthat", "caTools", "corrplot", "data_table", "dplyr", "ggplot2", "pheatmap", "pscl", "purrr", "reshape2", "viridis"] 10301 }, 10302 "missMethyl": { 10303 "name": "missMethyl", 10304 "version": "1.44.0", 10305 "sha256": "1kdy34wvvdvcjxxp0jkj3c54g14pi5qnq3vzs8ywxinf2a45vyiy", 10306 "depends": ["AnnotationDbi", "BiasedUrn", "Biobase", "BiocGenerics", "GO_db", "GenomeInfoDb", "GenomicRanges", "IRanges", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno_ilm10b4_hg19", "IlluminaHumanMethylationEPICmanifest", "IlluminaHumanMethylationEPICv2anno_20a1_hg38", "IlluminaHumanMethylationEPICv2manifest", "S4Vectors", "SummarizedExperiment", "limma", "methylumi", "minfi", "org_Hs_eg_db", "ruv", "statmod", "stringr"] 10307 }, 10308 "missRows": { 10309 "name": "missRows", 10310 "version": "1.30.0", 10311 "sha256": "1p3hgp6w8rjaa83jk75c7f4qv1cblinc21sn88pp99lva7ml7ppr", 10312 "depends": ["MultiAssayExperiment", "S4Vectors", "ggplot2", "gtools", "plyr"] 10313 }, 10314 "mist": { 10315 "name": "mist", 10316 "version": "1.2.0", 10317 "sha256": "0s8k2zcjnmm9l8ndwa8acgjkhgmamglbhxy1mx8qrzhgc3ahfmys", 10318 "depends": ["BiocGenerics", "BiocParallel", "MCMCpack", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "car", "mvtnorm", "rlang", "rtracklayer"] 10319 }, 10320 "mistyR": { 10321 "name": "mistyR", 10322 "version": "1.18.0", 10323 "sha256": "0hrmw9lnz6pdqhvfmg5gkpx90k05iha5dgzqm30jxpbzq6jwaqcf", 10324 "depends": ["R_utils", "assertthat", "caret", "deldir", "digest", "distances", "dplyr", "filelock", "furrr", "ggplot2", "purrr", "ranger", "readr", "ridge", "rlang", "rlist", "stringr", "tibble", "tidyr", "tidyselect", "withr"] 10325 }, 10326 "mitch": { 10327 "name": "mitch", 10328 "version": "1.22.0", 10329 "sha256": "0lixshjjlahm25yn3qn67k12m2wmpd4gmk7vydx9l2shflnsqh41", 10330 "depends": ["GGally", "MASS", "beeswarm", "dplyr", "echarts4r", "ggplot2", "gplots", "gridExtra", "kableExtra", "knitr", "network", "plyr", "reshape2", "rmarkdown"] 10331 }, 10332 "mitoClone2": { 10333 "name": "mitoClone2", 10334 "version": "1.16.0", 10335 "sha256": "0rsz3f1gw39hzlf48a2vxsyasipff2dq7nfx4wxi3csr0v2sr7ds", 10336 "depends": ["GenomicRanges", "Matrix", "Rhtslib", "S4Vectors", "deepSNV", "ggplot2", "pheatmap", "reshape2"] 10337 }, 10338 "mitology": { 10339 "name": "mitology", 10340 "version": "1.2.0", 10341 "sha256": "0h8smm994dlbszw61858slhy99d3rsbx9fmlmflagvj28yiajz6z", 10342 "depends": ["AnnotationDbi", "ComplexHeatmap", "ReactomePA", "ape", "circlize", "clusterProfiler", "ggplot2", "ggtree", "magrittr", "org_Hs_eg_db", "scales"] 10343 }, 10344 "mixOmics": { 10345 "name": "mixOmics", 10346 "version": "6.34.0", 10347 "sha256": "059xfj1air49mfcig226lkicqmq33b4cn7x5m9wpz3qvwa9l3mr7", 10348 "depends": ["BiocParallel", "MASS", "RColorBrewer", "corpcor", "dplyr", "ellipse", "ggplot2", "ggrepel", "gridExtra", "gsignal", "igraph", "lattice", "matrixStats", "rARPACK", "reshape2", "rgl", "tidyr"] 10349 }, 10350 "mnem": { 10351 "name": "mnem", 10352 "version": "1.26.0", 10353 "sha256": "0crjbx3kzf2r06601n4f0dd6b46pm3f3azsffblh32rmny28c348", 10354 "depends": ["Linnorm", "Rcpp", "RcppEigen", "Rgraphviz", "cluster", "data_table", "e1071", "flexclust", "ggplot2", "graph", "lattice", "matrixStats", "naturalsort", "snowfall", "tsne", "wesanderson"] 10355 }, 10356 "moanin": { 10357 "name": "moanin", 10358 "version": "1.18.0", 10359 "sha256": "1l95lhknp72zzsg28jnfv421pvlqdx4mjarddv3blkc8bm72lp5r", 10360 "depends": ["ClusterR", "MASS", "NMI", "S4Vectors", "SummarizedExperiment", "edgeR", "limma", "matrixStats", "reshape2", "topGO", "viridis", "zoo"] 10361 }, 10362 "mobileRNA": { 10363 "name": "mobileRNA", 10364 "version": "1.5.1", 10365 "sha256": "136jliyz1iyf3ncwsval34rnhdgpfgsh2jsxijwnax9vk7q9dixm", 10366 "depends": ["BiocGenerics", "Biostrings", "DESeq2", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "Seqinfo", "SimDesign", "SummarizedExperiment", "bioseq", "data_table", "dplyr", "edgeR", "ggplot2", "ggrepel", "pheatmap", "progress", "reticulate", "rlang", "rtracklayer", "scales", "tidyr", "tidyselect"] 10367 }, 10368 "mogsa": { 10369 "name": "mogsa", 10370 "version": "1.44.0", 10371 "sha256": "05n8q7iw1qp1sxjvrh96wpynqv58jm3wiggwkpw0hygz95a5wkxn", 10372 "depends": ["Biobase", "BiocGenerics", "GSEABase", "cluster", "corpcor", "genefilter", "gplots", "graphite", "svd"] 10373 }, 10374 "monaLisa": { 10375 "name": "monaLisa", 10376 "version": "1.16.0", 10377 "sha256": "08sjacip97ng2bna1faz1gx98mjxnrskjb14al7l7f5wkc16mkki", 10378 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "ComplexHeatmap", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TFBSTools", "XVector", "circlize", "cli", "ggplot2", "glmnet", "rlang", "stabs", "tidyr"] 10379 }, 10380 "monocle": { 10381 "name": "monocle", 10382 "version": "2.38.0", 10383 "sha256": "1wcxr0c1w8d5fhn2lvd36w2c613c2hyhjbn7j7ai0mp7hbr61g2p", 10384 "depends": ["Biobase", "BiocGenerics", "DDRTree", "HSMMSingleCell", "MASS", "Matrix", "RANN", "Rcpp", "Rtsne", "VGAM", "biocViews", "cluster", "combinat", "dplyr", "fastICA", "ggplot2", "igraph", "irlba", "leidenbase", "limma", "matrixStats", "pheatmap", "plyr", "proxy", "reshape2", "slam", "stringr", "tibble", "viridis"] 10385 }, 10386 "mosaics": { 10387 "name": "mosaics", 10388 "version": "2.48.0", 10389 "sha256": "1fw8kkk3qgsffwrmcjrkjrq8l9hxilmjvgwxlspp3rzr0rwwc2v7", 10390 "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "Rcpp", "Rsamtools", "S4Vectors", "Seqinfo", "lattice"] 10391 }, 10392 "mosbi": { 10393 "name": "mosbi", 10394 "version": "1.16.0", 10395 "sha256": "1bpiy4kh3md4y8qfk5z9k503mp3jk0gwh1v7i82x890l5s4bxz01", 10396 "depends": ["BH", "QUBIC", "RColorBrewer", "Rcpp", "RcppParallel", "akmbiclust", "biclust", "fabia", "igraph", "isa2", "xml2"] 10397 }, 10398 "mosdef": { 10399 "name": "mosdef", 10400 "version": "1.6.0", 10401 "sha256": "0000gasgr2bc486wxygz4xinv2skvcp0p6qv8nlknimv8lz50cl8", 10402 "depends": ["AnnotationDbi", "DESeq2", "DT", "GO_db", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "clusterProfiler", "ggforce", "ggplot2", "ggrepel", "goseq", "htmltools", "rlang", "scales", "topGO"] 10403 }, 10404 "motifStack": { 10405 "name": "motifStack", 10406 "version": "1.54.0", 10407 "sha256": "0vx619mlissjm6bb878l2n8jd4cb9x3d96rqjb6kj3gi4b9sys4z", 10408 "depends": ["Biostrings", "TFBSTools", "XML", "ade4", "ggplot2", "htmlwidgets"] 10409 }, 10410 "motifTestR": { 10411 "name": "motifTestR", 10412 "version": "1.6.0", 10413 "sha256": "04db9zb2p3nh1md1dz8vl0428vr0m0dfvfdp5zzclww095dx78ff", 10414 "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "ggplot2", "harmonicmeanp", "matrixStats", "patchwork", "rlang", "universalmotif"] 10415 }, 10416 "motifbreakR": { 10417 "name": "motifbreakR", 10418 "version": "2.24.0", 10419 "sha256": "0ksxil00v1s282zvsj0gjzybq46kcfay849y2syh7la7pgdw3x63", 10420 "depends": ["BSgenome", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "DT", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "MotifDb", "S4Vectors", "SummarizedExperiment", "TFMPvalue", "VariantAnnotation", "biomaRt", "bsicons", "bslib", "matrixStats", "motifStack", "pwalign", "rtracklayer", "shiny", "stringr", "vroom"] 10421 }, 10422 "motifcounter": { 10423 "name": "motifcounter", 10424 "version": "1.34.0", 10425 "sha256": "1mbda7hccy43ar1ii5ldn2qvbvzbmdx686kic3y6kxd03frmjb94", 10426 "depends": ["Biostrings"] 10427 }, 10428 "motifmatchr": { 10429 "name": "motifmatchr", 10430 "version": "1.32.0", 10431 "sha256": "16crqy7y6iad4b29mgxisf7gp06snf7bxgkm3y06f66y8faajlyk", 10432 "depends": ["BSgenome", "Biostrings", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "RcppArmadillo", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "TFBSTools"] 10433 }, 10434 "mpra": { 10435 "name": "mpra", 10436 "version": "1.32.0", 10437 "sha256": "0yqk8h7l7q4q0g4h39q1gbsfb1lqvcxrfbmn2wnl6chzbf71yszd", 10438 "depends": ["BiocGenerics", "S4Vectors", "SummarizedExperiment", "limma", "scales", "statmod"] 10439 }, 10440 "msImpute": { 10441 "name": "msImpute", 10442 "version": "1.20.0", 10443 "sha256": "1gjh519b7adrczha2cfh33yqg6rz3fn27m5bydqkf1gw5hilq9wx", 10444 "depends": ["FNN", "data_table", "dplyr", "limma", "matrixStats", "mvtnorm", "pdist", "reticulate", "scran", "softImpute", "tidyr"] 10445 }, 10446 "msPurity": { 10447 "name": "msPurity", 10448 "version": "1.36.0", 10449 "sha256": "004wmqqxdpdbhax112v4hidp1bxyq3h8c307cvryyz4gahqfsr0p", 10450 "depends": ["DBI", "RSQLite", "Rcpp", "dbplyr", "doSNOW", "dplyr", "fastcluster", "foreach", "ggplot2", "magrittr", "mzR", "plyr", "reshape2", "stringr"] 10451 }, 10452 "msa": { 10453 "name": "msa", 10454 "version": "1.42.0", 10455 "sha256": "0ch5ghyg2wswsywwnrxjcn7dayvm9mxfnww9l38k458r6iw8s7a5", 10456 "depends": ["BiocGenerics", "Biostrings", "IRanges", "Rcpp", "S4Vectors"] 10457 }, 10458 "msgbsR": { 10459 "name": "msgbsR", 10460 "version": "1.34.0", 10461 "sha256": "12gbzwvf5rdv8dl29wi8qrrzvl62vncd8q76h3x5bxwbp4dnjzrd", 10462 "depends": ["BSgenome", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "easyRNASeq", "edgeR", "ggbio", "ggplot2", "plyr"] 10463 }, 10464 "mslp": { 10465 "name": "mslp", 10466 "version": "1.12.0", 10467 "sha256": "0pfncr3fdcccd8pi73l5n3qpwg4m2a53grsk8izm5839xc16mwpq", 10468 "depends": ["RankProd", "data_table", "doRNG", "fmsb", "foreach", "magrittr", "org_Hs_eg_db", "pROC", "randomForest"] 10469 }, 10470 "msmsEDA": { 10471 "name": "msmsEDA", 10472 "version": "1.48.0", 10473 "sha256": "1pvqw3py9hajk2dx7bwbpw4lqb0m0p9ir6l8wp7hmi0w1gv5grl4", 10474 "depends": ["MASS", "MSnbase", "RColorBrewer", "gplots"] 10475 }, 10476 "msmsTests": { 10477 "name": "msmsTests", 10478 "version": "1.48.0", 10479 "sha256": "1g2fbl1x598yc2s81jb95ksw6mfp8yv5vsq8znndazf9zlfnm6r3", 10480 "depends": ["MSnbase", "edgeR", "msmsEDA", "qvalue"] 10481 }, 10482 "mspms": { 10483 "name": "mspms", 10484 "version": "1.2.0", 10485 "sha256": "1nipbivljfcr87lfxp2iz6x2zfambk4s7jqyv951vywlq3p8f6pb", 10486 "depends": ["QFeatures", "SummarizedExperiment", "dplyr", "ggplot2", "ggpubr", "ggseqlogo", "heatmaply", "limma", "magrittr", "purrr", "readr", "rlang", "rstatix", "stringr", "tibble", "tidyr"] 10487 }, 10488 "msqrob2": { 10489 "name": "msqrob2", 10490 "version": "1.18.0", 10491 "sha256": "0kd452vjwzqizfmqma7770bfcdsn22hk9xfhs37zqj806cadc0sn", 10492 "depends": ["BiocParallel", "MASS", "Matrix", "MultiAssayExperiment", "QFeatures", "SummarizedExperiment", "codetools", "limma", "lme4", "purrr"] 10493 }, 10494 "multiClust": { 10495 "name": "multiClust", 10496 "version": "1.40.0", 10497 "sha256": "0xpjx9wv2vkq3r2r1lpjvagac93hrw9q1r3y32zzk05pakrn5fxr", 10498 "depends": ["amap", "cluster", "ctc", "dendextend", "mclust", "survival"] 10499 }, 10500 "multiGSEA": { 10501 "name": "multiGSEA", 10502 "version": "1.20.0", 10503 "sha256": "0z2pscdc1il9lywckadyv3ljqkijhi4xfdvaks2z7p3dsrxs14sw", 10504 "depends": ["AnnotationDbi", "dplyr", "fgsea", "graphite", "magrittr", "metaboliteIDmapping", "metap", "rappdirs", "rlang"] 10505 }, 10506 "multiHiCcompare": { 10507 "name": "multiHiCcompare", 10508 "version": "1.28.0", 10509 "sha256": "10vqacbx18vwdk23zkib9ccbs47vpvj8x7sbckhnan9y4zvdfd1j", 10510 "depends": ["BiocParallel", "GenomeInfoDb", "GenomeInfoDbData", "GenomicRanges", "HiCcompare", "aggregation", "data_table", "dplyr", "edgeR", "pbapply", "pheatmap", "qqman"] 10511 }, 10512 "multiMiR": { 10513 "name": "multiMiR", 10514 "version": "1.32.0", 10515 "sha256": "02dj6aslq2vaafdsd3rfvlbfdg7bahy214w3ld0yi22chypm5m29", 10516 "depends": ["AnnotationDbi", "BiocGenerics", "RCurl", "XML", "dplyr", "purrr", "tibble"] 10517 }, 10518 "multiWGCNA": { 10519 "name": "multiWGCNA", 10520 "version": "1.7.0", 10521 "sha256": "06njw4dz3fjh6g703z2k2cphrvmwf4azfg4w86iin6j67f361vz1", 10522 "depends": ["SummarizedExperiment", "WGCNA", "cowplot", "data_table", "dcanr", "dplyr", "flashClust", "ggalluvial", "ggplot2", "ggrepel", "igraph", "patchwork", "readr", "reshape2", "scales", "stringr"] 10523 }, 10524 "multicrispr": { 10525 "name": "multicrispr", 10526 "version": "1.20.0", 10527 "sha256": "06ac6r9psmwx65x64clbsmsw6kzbdsbxvw9y1da23pzs37fpd1cc", 10528 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "CRISPRseek", "GenomicFeatures", "GenomicRanges", "Rbowtie", "Seqinfo", "data_table", "ggplot2", "karyoploteR", "magrittr", "plyranges", "reticulate", "rtracklayer", "stringi", "tidyr", "tidyselect"] 10529 }, 10530 "multiscan": { 10531 "name": "multiscan", 10532 "version": "1.70.0", 10533 "sha256": "1spl6myhmn8zkhif8bwvdlzhm4jc648qlw928xlc60v2x5y3qb3b", 10534 "depends": ["Biobase"] 10535 }, 10536 "multistateQTL": { 10537 "name": "multistateQTL", 10538 "version": "2.2.0", 10539 "sha256": "0jllxhr2pnd4p2yhpplnf784k0gcg3zh5k7593mpxcpjgrhp87b5", 10540 "depends": ["ComplexHeatmap", "QTLExperiment", "S4Vectors", "SummarizedExperiment", "circlize", "collapse", "data_table", "dplyr", "fitdistrplus", "ggplot2", "mashr", "matrixStats", "tidyr", "viridis"] 10541 }, 10542 "multtest": { 10543 "name": "multtest", 10544 "version": "2.66.0", 10545 "sha256": "1jc5q1amr2q980xpa7ysp7vg9ihmypv16ph4p8jgpj4jdr1dl71h", 10546 "depends": ["Biobase", "BiocGenerics", "MASS", "survival"] 10547 }, 10548 "mumosa": { 10549 "name": "mumosa", 10550 "version": "1.18.0", 10551 "sha256": "16p50lz5qnpdaa56h98a01czsn1pz12mm6z0426qz2yp14wmmi2q", 10552 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "IRanges", "Matrix", "S4Vectors", "ScaledMatrix", "SingleCellExperiment", "SummarizedExperiment", "batchelor", "beachmat", "igraph", "metapod", "scran", "scuttle", "uwot"] 10553 }, 10554 "muscat": { 10555 "name": "muscat", 10556 "version": "1.24.0", 10557 "sha256": "0nv0qrw3cvzf6j4li2ln4xw2afdlzlpy7fn5b9cpf9g8cyn6qcqj", 10558 "depends": ["BiocParallel", "ComplexHeatmap", "DESeq2", "IHW", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "blme", "data_table", "dplyr", "edgeR", "ggplot2", "glmmTMB", "limma", "lme4", "lmerTest", "matrixStats", "progress", "purrr", "rlang", "scales", "scater", "sctransform", "scuttle", "variancePartition"] 10559 }, 10560 "muscle": { 10561 "name": "muscle", 10562 "version": "3.52.0", 10563 "sha256": "08ajymh02nlsa3ks5qhnz3d59a1mdsn6vgyslzvib6g0x6ka7z42", 10564 "depends": ["Biostrings"] 10565 }, 10566 "musicatk": { 10567 "name": "musicatk", 10568 "version": "2.4.0", 10569 "sha256": "1a3npb4b5a10jp09bx53636hv1xbw2fw60k0iqs7hr7r85rd25m1", 10570 "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BSgenome_Mmusculus_UCSC_mm10", "BSgenome_Mmusculus_UCSC_mm9", "Biostrings", "ComplexHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "MCMCprecision", "Matrix", "NMF", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "VariantAnnotation", "cluster", "data_table", "decompTumor2Sig", "dplyr", "factoextra", "ggplot2", "ggpubr", "ggrepel", "gridExtra", "gtools", "maftools", "magrittr", "matrixTests", "philentropy", "plotly", "rlang", "scales", "shiny", "stringi", "stringr", "tibble", "tidyr", "tidyverse", "topicmodels", "uwot"] 10571 }, 10572 "mutscan": { 10573 "name": "mutscan", 10574 "version": "1.0.0", 10575 "sha256": "1xqfbljy61ir2blglvisqbgyn490mxbn6kfn68l0cjkvpz13wl51", 10576 "depends": ["BiocGenerics", "DT", "DelayedArray", "GGally", "IRanges", "Matrix", "Rcpp", "S4Vectors", "SummarizedExperiment", "csaw", "dplyr", "edgeR", "ggplot2", "ggrepel", "limma", "rlang", "rmarkdown", "tibble", "tidyr", "tidyselect", "xfun"] 10577 }, 10578 "mygene": { 10579 "name": "mygene", 10580 "version": "1.46.0", 10581 "sha256": "0a142c95975yphffn8xcg76j0l0ywjw2h0r6jqpm65knhhrn009s", 10582 "depends": ["GenomicFeatures", "Hmisc", "S4Vectors", "httr", "jsonlite", "plyr", "sqldf", "txdbmaker"] 10583 }, 10584 "myvariant": { 10585 "name": "myvariant", 10586 "version": "1.40.0", 10587 "sha256": "0lfpkl5y22gg4185ldgkc0y4jxpyvdl83mnzmj9m2qprszbk69r8", 10588 "depends": ["GenomeInfoDb", "Hmisc", "S4Vectors", "Seqinfo", "VariantAnnotation", "httr", "jsonlite", "magrittr", "plyr"] 10589 }, 10590 "mzID": { 10591 "name": "mzID", 10592 "version": "1.48.0", 10593 "sha256": "13lav2pfn03r42krxr6mc8rm332plfs081yf18vnw69pxq0vxw43", 10594 "depends": ["ProtGenerics", "XML", "doParallel", "foreach", "iterators", "plyr"] 10595 }, 10596 "mzR": { 10597 "name": "mzR", 10598 "version": "2.44.0", 10599 "sha256": "049mvigh03bdiic82ryw7cwqmgzm8ivhdv5pfs6rggaaba3awc42", 10600 "depends": ["Biobase", "BiocGenerics", "ProtGenerics", "Rcpp", "Rhdf5lib", "ncdf4"] 10601 }, 10602 "ncGTW": { 10603 "name": "ncGTW", 10604 "version": "1.24.0", 10605 "sha256": "0nipay8lx0dnd2ix8sr84idazhbmc1zryh75hpry9irh80x395nb", 10606 "depends": ["BiocParallel", "Rcpp", "xcms"] 10607 }, 10608 "ncRNAtools": { 10609 "name": "ncRNAtools", 10610 "version": "1.20.0", 10611 "sha256": "1zm9qfaj6pcy9y9bb80inhawmdk94a2ps603hwxpgpaa9s701if9", 10612 "depends": ["GenomicRanges", "IRanges", "S4Vectors", "ggplot2", "httr", "xml2"] 10613 }, 10614 "ncdfFlow": { 10615 "name": "ncdfFlow", 10616 "version": "2.56.0", 10617 "sha256": "0431c0yxdzaq665rd59ljlsijhqx435l0zpbviy74nkcbmgip1js", 10618 "depends": ["BH", "Biobase", "BiocGenerics", "Rhdf5lib", "cpp11", "flowCore"] 10619 }, 10620 "ndexr": { 10621 "name": "ndexr", 10622 "version": "1.32.0", 10623 "sha256": "16a9b4bqx877xsbk8pw9dmg3n5g7m0ych5jd1li1ljczxz4wmkql", 10624 "depends": ["RCX", "httr", "jsonlite", "plyr", "tidyr"] 10625 }, 10626 "nearBynding": { 10627 "name": "nearBynding", 10628 "version": "1.20.0", 10629 "sha256": "0cl46qbm8vm6yphjn8xxva3qp7xak780b8r655111dc986xk9d5w", 10630 "depends": ["BiocGenerics", "GenomicRanges", "R_utils", "Rsamtools", "S4Vectors", "Seqinfo", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "dplyr", "ggplot2", "gplots", "magrittr", "matrixStats", "plyranges", "rlang", "rtracklayer", "transport"] 10631 }, 10632 "nempi": { 10633 "name": "nempi", 10634 "version": "1.18.0", 10635 "sha256": "0naphfkdmvxshz1fh35ki5p00kd030afav67cmnk1j5sv06rysa4", 10636 "depends": ["e1071", "epiNEM", "matrixStats", "mnem", "naturalsort", "nnet", "randomForest"] 10637 }, 10638 "netSmooth": { 10639 "name": "netSmooth", 10640 "version": "1.30.0", 10641 "sha256": "0hmji08nyfbb278r76dpix0qlbhn1rr9vyjjc6lx0f8qvsz4cbis", 10642 "depends": ["DelayedArray", "HDF5Array", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "cluster", "clusterExperiment", "data_table", "entropy", "scater"] 10643 }, 10644 "netboost": { 10645 "name": "netboost", 10646 "version": "2.18.0", 10647 "sha256": "0kqix8n5gr79hzizfwbg78l61zqkgmpjhgvlyb2h4sl7ka1m0rna", 10648 "depends": ["BiocStyle", "R_utils", "Rcpp", "RcppParallel", "WGCNA", "colorspace", "dynamicTreeCut", "impute"] 10649 }, 10650 "nethet": { 10651 "name": "nethet", 10652 "version": "1.42.0", 10653 "sha256": "0l5d5sm5wclhyv5brwzimlzb50dn9y6ls1appm2d0wnl9h806g5z", 10654 "depends": ["CompQuadForm", "GSA", "GeneNet", "ICSNP", "ggm", "ggplot2", "glasso", "glmnet", "huge", "limma", "mclust", "multtest", "mvtnorm", "network"] 10655 }, 10656 "netprioR": { 10657 "name": "netprioR", 10658 "version": "1.36.0", 10659 "sha256": "1qi6nxg53pn8fkm9m4rffzrq0v6zh43057n4686c2p1knqfmz8a1", 10660 "depends": ["Matrix", "doParallel", "dplyr", "foreach", "ggplot2", "gridExtra", "pROC", "sparseMVN"] 10661 }, 10662 "netresponse": { 10663 "name": "netresponse", 10664 "version": "1.70.0", 10665 "sha256": "0i7wbgx6yfcf1j2b7xwlg6ac59gjfvlxsgiq94v57ikvmplvhzh1", 10666 "depends": ["BiocStyle", "RColorBrewer", "Rgraphviz", "ggplot2", "graph", "igraph", "mclust", "minet", "plyr", "qvalue", "reshape2", "rmarkdown"] 10667 }, 10668 "ngsReports": { 10669 "name": "ngsReports", 10670 "version": "2.12.0", 10671 "sha256": "07cmycg3vs4h6r06aq56r3h4ckr3fyaw0mmic29p6a5kz5b19zq3", 10672 "depends": ["BiocGenerics", "Biostrings", "checkmate", "dplyr", "forcats", "ggdendro", "ggplot2", "jsonlite", "lifecycle", "lubridate", "patchwork", "plotly", "rlang", "rmarkdown", "scales", "stringr", "tibble", "tidyr", "tidyselect", "zoo"] 10673 }, 10674 "nipalsMCIA": { 10675 "name": "nipalsMCIA", 10676 "version": "1.8.0", 10677 "sha256": "1njd24qvzb3pp94rcadb4dn7h7q79s1ifizrw1b5hxc4lv19fxmr", 10678 "depends": ["ComplexHeatmap", "MultiAssayExperiment", "RSpectra", "SummarizedExperiment", "dplyr", "fgsea", "ggplot2", "pracma", "rlang", "scales"] 10679 }, 10680 "nnNorm": { 10681 "name": "nnNorm", 10682 "version": "2.74.0", 10683 "sha256": "13cvpnfj3jglwnrpb301qi2lhkbgim9q0q0nzv02iwydg3034w06", 10684 "depends": ["marray", "nnet"] 10685 }, 10686 "nnSVG": { 10687 "name": "nnSVG", 10688 "version": "1.14.0", 10689 "sha256": "1l4vnydyi65z6xac7scpcm7rrhgplcx9jpsjnm7npf1pi4hp6wm2", 10690 "depends": ["BRISC", "BiocParallel", "Matrix", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "matrixStats"] 10691 }, 10692 "nondetects": { 10693 "name": "nondetects", 10694 "version": "2.40.0", 10695 "sha256": "0rslx17l1rd1fmb5phwknlwjpp832qg8h3pcap11nw9wzisxa5dk", 10696 "depends": ["Biobase", "HTqPCR", "arm", "limma", "mvtnorm"] 10697 }, 10698 "normalize450K": { 10699 "name": "normalize450K", 10700 "version": "1.38.0", 10701 "sha256": "19bw5v7h7m4y2kzqj92rigs048ha7cqgxjnl2bqz5sq2axcqknzh", 10702 "depends": ["Biobase", "illuminaio", "quadprog"] 10703 }, 10704 "normr": { 10705 "name": "normr", 10706 "version": "1.36.0", 10707 "sha256": "1knfcwrjwp6nv4pdhvihxad7xpl5pba07x9n1rsmddn6q3nhgq5l", 10708 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rcpp", "bamsignals", "qvalue", "rtracklayer"] 10709 }, 10710 "notame": { 10711 "name": "notame", 10712 "version": "1.0.0", 10713 "sha256": "0dyqnjci0nc8k56hqhs9wm6xlzn593m8bprhsc4jvylpxlfi64vv", 10714 "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SummarizedExperiment", "dplyr", "futile_logger", "ggplot2", "openxlsx", "scales", "stringr", "tidyr"] 10715 }, 10716 "notameStats": { 10717 "name": "notameStats", 10718 "version": "1.0.0", 10719 "sha256": "1kw8a12z0qz5hxpwlghl4ynvwv9rpdkm8115fs591a55ppzn1rga", 10720 "depends": ["BiocGenerics", "BiocParallel", "SummarizedExperiment", "broom", "dplyr", "notame", "tibble", "tidyr"] 10721 }, 10722 "notameViz": { 10723 "name": "notameViz", 10724 "version": "1.0.0", 10725 "sha256": "0hs3ckg0wff74zvmmcxpbkncxnz8hxm79vrjmzy3gfy0iwww1lhf", 10726 "depends": ["BiocGenerics", "SummarizedExperiment", "cowplot", "devEMF", "dplyr", "ggbeeswarm", "ggdendro", "ggplot2", "ggrepel", "notame", "scales", "stringr", "tibble", "tidyr"] 10727 }, 10728 "npGSEA": { 10729 "name": "npGSEA", 10730 "version": "1.46.0", 10731 "sha256": "0p5d8fff2m7sgzkmasf014izjh21cbkzv5gi99ppfid8dv0p7srn", 10732 "depends": ["Biobase", "BiocGenerics", "GSEABase"] 10733 }, 10734 "nuCpos": { 10735 "name": "nuCpos", 10736 "version": "1.28.0", 10737 "sha256": "07ndp9xrx9s62cajrd6d5p5y89lkmwcrbwwmbf1pz0q11ylfcd8h", 10738 "depends": [] 10739 }, 10740 "nucleR": { 10741 "name": "nucleR", 10742 "version": "2.42.0", 10743 "sha256": "04al07jhszkmgszpzyv9vy8dsj333h4awghznqpalifmqady2bn4", 10744 "depends": ["Biobase", "BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "ShortRead", "dplyr", "ggplot2", "magrittr"] 10745 }, 10746 "nucleoSim": { 10747 "name": "nucleoSim", 10748 "version": "1.38.0", 10749 "sha256": "0f8yzw8w30kfzxanyianffhavricc9l864fda7fg8wl4jsbhpgyv", 10750 "depends": ["IRanges", "S4Vectors"] 10751 }, 10752 "nullranges": { 10753 "name": "nullranges", 10754 "version": "1.16.0", 10755 "sha256": "11mdbshvsg5d60gqa9alr43h2kwz0s35pwf5ibs4z5yfry2h3hhs", 10756 "depends": ["GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "Seqinfo", "data_table", "ggplot2", "ggridges", "plyranges", "progress", "rlang", "scales"] 10757 }, 10758 "occugene": { 10759 "name": "occugene", 10760 "version": "1.70.0", 10761 "sha256": "0s4lkpwd34rfp6rhhjsgm8m5gqqcy7cmlq4x1qm3iw6fpkqgvv9i", 10762 "depends": [] 10763 }, 10764 "octad": { 10765 "name": "octad", 10766 "version": "1.12.0", 10767 "sha256": "0ck5hm6h83cish09ha65m000bvciws5bb3a707wc9kcxcsy08g1k", 10768 "depends": ["AnnotationHub", "Biobase", "DESeq2", "EDASeq", "ExperimentHub", "GSVA", "RUVSeq", "Rfast", "S4Vectors", "data_table", "dplyr", "edgeR", "foreach", "ggplot2", "htmlwidgets", "httr", "limma", "magrittr", "octad_db", "plotly", "qpdf", "reshape2", "rhdf5"] 10769 }, 10770 "odseq": { 10771 "name": "odseq", 10772 "version": "1.38.0", 10773 "sha256": "0v7j3fnpphbbmqmm96iqyz7rhv5bkx10qrikkg2zj24k4h7br18p", 10774 "depends": ["kebabs", "mclust", "msa"] 10775 }, 10776 "oligo": { 10777 "name": "oligo", 10778 "version": "1.74.0", 10779 "sha256": "07kkssywxinqbkpwgjihk2lia25kgr26vdbb5icwb7xldff9s4x1", 10780 "depends": ["Biobase", "BiocGenerics", "Biostrings", "DBI", "RSQLite", "affxparser", "affyio", "bit", "ff", "oligoClasses", "preprocessCore"] 10781 }, 10782 "oligoClasses": { 10783 "name": "oligoClasses", 10784 "version": "1.72.0", 10785 "sha256": "11sy2zpjj8h2wf5qjmfxq07b5bk8y58vbqr06dr9ymk3bgwwp0c8", 10786 "depends": ["Biobase", "BiocGenerics", "BiocManager", "Biostrings", "DBI", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "SummarizedExperiment", "affyio", "ff", "foreach"] 10787 }, 10788 "omXplore": { 10789 "name": "omXplore", 10790 "version": "1.3.0", 10791 "sha256": "02lrmskpg560yh0aadsx6b822in3s5fvldl52ncly8pckbs7rpc8", 10792 "depends": ["DT", "FactoMineR", "MSnbase", "MultiAssayExperiment", "PSMatch", "RColorBrewer", "SummarizedExperiment", "bs4Dash", "dendextend", "dplyr", "factoextra", "gplots", "highcharter", "htmlwidgets", "nipals", "shiny", "shinyBS", "shinyjqui", "shinyjs", "thematic", "tibble", "tidyr", "vioplot", "visNetwork", "waiter"] 10793 }, 10794 "omada": { 10795 "name": "omada", 10796 "version": "1.12.0", 10797 "sha256": "047lmy4c5fawz9pxnjv62jxzrb50p4vajsrnsqrxgsa5ch0rsjhs", 10798 "depends": ["Rcpp", "clValid", "diceR", "dplyr", "fpc", "genieclust", "ggplot2", "glmnet", "kernlab", "pdfCluster", "reshape"] 10799 }, 10800 "omicRexposome": { 10801 "name": "omicRexposome", 10802 "version": "1.32.0", 10803 "sha256": "0244dnay1ilgsrpp9ppcr94fw7d2xaiqlcmc6bqlfd739gi8nldx", 10804 "depends": ["Biobase", "MultiDataSet", "PMA", "SmartSVA", "SummarizedExperiment", "ggplot2", "ggrepel", "gridExtra", "isva", "limma", "omicade4", "rexposome", "stringr", "sva"] 10805 }, 10806 "omicade4": { 10807 "name": "omicade4", 10808 "version": "1.50.0", 10809 "sha256": "16v3hb9a980yzy05my0l14r76k1lap69zpzjndrdwp114glbhlpl", 10810 "depends": ["Biobase", "ade4", "made4"] 10811 }, 10812 "omicplotR": { 10813 "name": "omicplotR", 10814 "version": "1.30.0", 10815 "sha256": "1n8f10z1r4z0q1b8qhklic7ylini5sas35i2c9snd6gllbv2ldl1", 10816 "depends": ["ALDEx2", "DT", "compositions", "jsonlite", "knitr", "matrixStats", "rmarkdown", "shiny", "vegan", "zCompositions"] 10817 }, 10818 "omicsGMF": { 10819 "name": "omicsGMF", 10820 "version": "1.0.0", 10821 "sha256": "09bxkgf5qw86avbivqx2nr0apgrgs2f19gy00cwp0mprrvdnc136", 10822 "depends": ["BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "MatrixGenerics", "QFeatures", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "beachmat", "ggplot2", "scater", "scuttle", "sgdGMF"] 10823 }, 10824 "omicsPrint": { 10825 "name": "omicsPrint", 10826 "version": "1.30.0", 10827 "sha256": "1714n5ijcryiyamr514rhcxq4wk37d49ad96ginhsxm3x6cals38", 10828 "depends": ["MASS", "MultiAssayExperiment", "RaggedExperiment", "SummarizedExperiment", "matrixStats"] 10829 }, 10830 "omicsViewer": { 10831 "name": "omicsViewer", 10832 "version": "1.14.0", 10833 "sha256": "1xnz0325s1cbfda3j77pqw4cnjh22rdb13rw4jdkwnxmr2qmc2ic", 10834 "depends": ["Biobase", "DT", "Matrix", "RColorBrewer", "ROCR", "RSQLite", "S4Vectors", "SummarizedExperiment", "beeswarm", "curl", "drc", "fastmatch", "fgsea", "flatxml", "ggplot2", "ggseqlogo", "htmlwidgets", "httr", "matrixStats", "networkD3", "openxlsx", "plotly", "psych", "reshape2", "shiny", "shinyWidgets", "shinybusy", "shinycssloaders", "shinyjs", "shinythemes", "stringr", "survival", "survminer"] 10835 }, 10836 "ompBAM": { 10837 "name": "ompBAM", 10838 "version": "1.14.0", 10839 "sha256": "0qm0v3cqwc88n8l74s6lz7qa5lbfkgppag2l57k9666ry4g5j4av", 10840 "depends": ["Rcpp"] 10841 }, 10842 "oncomix": { 10843 "name": "oncomix", 10844 "version": "1.32.0", 10845 "sha256": "0va465rh4405g5vsy1vwhr76gc403smi6d1b3a9gclxpsg1a2ga6", 10846 "depends": ["RColorBrewer", "SummarizedExperiment", "ggplot2", "ggrepel", "mclust"] 10847 }, 10848 "oncoscanR": { 10849 "name": "oncoscanR", 10850 "version": "1.12.0", 10851 "sha256": "1nl9r29drgc22vyiqg02a3y7jf6qvkxg5m3lmcvccjb12m5986qm", 10852 "depends": ["GenomicRanges", "IRanges", "S4Vectors", "magrittr", "readr"] 10853 }, 10854 "onlineFDR": { 10855 "name": "onlineFDR", 10856 "version": "2.18.0", 10857 "sha256": "0669chhzkqa9giccaxlvv02rfbjfy2b8j6rc131qxic6p8s6ni66", 10858 "depends": ["Rcpp", "RcppProgress", "progress"] 10859 }, 10860 "ontoProc": { 10861 "name": "ontoProc", 10862 "version": "2.4.0", 10863 "sha256": "0wyw6gw6vwcya27w7fy11yxy9qf9wcfr5q5hx7sr86czkzrxa6fc", 10864 "depends": ["AnnotationHub", "Biobase", "BiocFileCache", "DT", "RBGL", "R_utils", "Rgraphviz", "S4Vectors", "SummarizedExperiment", "basilisk", "dplyr", "ellmer", "graph", "httr", "igraph", "jsonlite", "magrittr", "ontologyIndex", "ontologyPlot", "reticulate", "shiny"] 10865 }, 10866 "openCyto": { 10867 "name": "openCyto", 10868 "version": "2.22.0", 10869 "sha256": "0sd2p8cya949zi9bf7hj2xy7kmkbvpviaxpfm3vb81ffk26z14gk", 10870 "depends": ["BH", "Biobase", "BiocGenerics", "RBGL", "RColorBrewer", "cpp11", "data_table", "flowClust", "flowCore", "flowViz", "flowWorkspace", "graph", "ncdfFlow"] 10871 }, 10872 "openPrimeR": { 10873 "name": "openPrimeR", 10874 "version": "1.32.0", 10875 "sha256": "0mv43d41p3isif7mpihp0ayk2izk79b6nws90700dhs5hkh24dq4", 10876 "depends": ["BiocGenerics", "Biostrings", "DECIPHER", "GenomicRanges", "Hmisc", "IRanges", "RColorBrewer", "S4Vectors", "XML", "ape", "digest", "dplyr", "foreach", "ggplot2", "lpSolveAPI", "magrittr", "openxlsx", "plyr", "pwalign", "reshape2", "scales", "seqinr", "stringdist", "stringr", "uniqtag"] 10877 }, 10878 "oposSOM": { 10879 "name": "oposSOM", 10880 "version": "2.28.0", 10881 "sha256": "0vwiizxy57xz4ha6nvpkyd5nr63p03mw3n33sq4i3pvyygbm4afj", 10882 "depends": ["Biobase", "RCurl", "Rcpp", "RcppParallel", "XML", "ape", "biomaRt", "fastICA", "fdrtool", "graph", "igraph", "pixmap", "png", "scatterplot3d", "tsne"] 10883 }, 10884 "oppar": { 10885 "name": "oppar", 10886 "version": "1.38.0", 10887 "sha256": "1g9ddbw0hzypw4ipyj6llvgq7mlmff27kzqfnd6nzgym8qpjk4d8", 10888 "depends": ["Biobase", "GSEABase", "GSVA"] 10889 }, 10890 "optimalFlow": { 10891 "name": "optimalFlow", 10892 "version": "1.22.0", 10893 "sha256": "13nz1583xkr0f6y2l4hmbjb2w9s0ir5bn5r3qcnpxn0yvy5iabgx", 10894 "depends": ["Rfast", "dbscan", "doParallel", "dplyr", "ellipse", "flowMeans", "foreach", "optimalFlowData", "randomForest", "rgl", "rlang", "robustbase", "transport"] 10895 }, 10896 "orthogene": { 10897 "name": "orthogene", 10898 "version": "1.16.0", 10899 "sha256": "00ixwgdmjyp7x3p9d4r9da777i7zrys9wilz8lm930cv5bcqsm06", 10900 "depends": ["DelayedArray", "Matrix", "babelgene", "data_table", "dplyr", "ggplot2", "ggpubr", "ggtree", "gprofiler2", "grr", "homologene", "jsonlite", "patchwork", "repmis"] 10901 }, 10902 "orthos": { 10903 "name": "orthos", 10904 "version": "1.8.0", 10905 "sha256": "1nyxc7b1gnfb9js4a6v1r3i7cs8wy9qqy5k7zjal27f3s99cdplr", 10906 "depends": ["AnnotationHub", "BiocParallel", "DelayedArray", "ExperimentHub", "HDF5Array", "S4Vectors", "SummarizedExperiment", "basilisk", "colorspace", "cowplot", "dplyr", "ggplot2", "ggpubr", "ggrepel", "ggsci", "keras", "orthosData", "plyr", "reticulate", "rlang", "tensorflow", "tidyr"] 10907 }, 10908 "pRoloc": { 10909 "name": "pRoloc", 10910 "version": "1.50.0", 10911 "sha256": "08anricap3nkdfc4k8rkc1gw1qcx990sy1z4lbvf1i1wh98dgzlp", 10912 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "FNN", "LaplacesDemon", "MASS", "MLInterfaces", "MSnbase", "RColorBrewer", "Rcpp", "RcppArmadillo", "biomaRt", "caret", "class", "coda", "colorspace", "dendextend", "e1071", "ggplot2", "gtools", "hexbin", "kernlab", "knitr", "lattice", "mclust", "mixtools", "mvtnorm", "nnet", "plyr", "proxy", "randomForest", "sampling", "scales"] 10913 }, 10914 "pRolocGUI": { 10915 "name": "pRolocGUI", 10916 "version": "2.20.0", 10917 "sha256": "05qcpz6y528al8kfxhv330gin970dvs7gbl9bw8l3lnbk1l8vg4a", 10918 "depends": ["Biobase", "BiocGenerics", "DT", "MSnbase", "colorspace", "colourpicker", "dplyr", "ggplot2", "pRoloc", "scales", "shiny", "shinyWidgets", "shinydashboard", "shinydashboardPlus", "shinyhelper", "shinyjs"] 10919 }, 10920 "packFinder": { 10921 "name": "packFinder", 10922 "version": "1.22.0", 10923 "sha256": "0hl8s4g0v4l5xy5dngr6zjjwbbbz6wr27qwy1win87khfnxsjilr", 10924 "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "ape", "kmer"] 10925 }, 10926 "padma": { 10927 "name": "padma", 10928 "version": "1.20.0", 10929 "sha256": "0mhy9cm7xfl4c6wnvhrmddvn6d4kplpv1fzcwx3ph2ii2ai4w5l5", 10930 "depends": ["FactoMineR", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment"] 10931 }, 10932 "pageRank": { 10933 "name": "pageRank", 10934 "version": "1.20.0", 10935 "sha256": "1rfa57k71xzy7ccbyk77nrsxpvz0xb6mnrnazzrssz7q007i209x", 10936 "depends": ["GenomicRanges", "igraph", "motifmatchr"] 10937 }, 10938 "paircompviz": { 10939 "name": "paircompviz", 10940 "version": "1.48.0", 10941 "sha256": "08dw95ny9lxgjz1wk4xsgggkgnvpp1wd4svl43499hnsgc92i60j", 10942 "depends": ["Rgraphviz"] 10943 }, 10944 "pairedGSEA": { 10945 "name": "pairedGSEA", 10946 "version": "1.10.0", 10947 "sha256": "1gkgkcajnm2m2277lnkdwyg6107w5d7089ba2gh8dbl5q9krbka2", 10948 "depends": ["BiocParallel", "DESeq2", "DEXSeq", "S4Vectors", "SummarizedExperiment", "aggregation", "fgsea", "ggplot2", "limma", "msigdbr", "showtext", "sva"] 10949 }, 10950 "pairkat": { 10951 "name": "pairkat", 10952 "version": "1.16.0", 10953 "sha256": "18h2ykss8x6j7gg0apbirvigh386v4hyli5m2hyfza46ncxllnvw", 10954 "depends": ["CompQuadForm", "KEGGREST", "SummarizedExperiment", "data_table", "igraph", "magrittr", "tibble"] 10955 }, 10956 "pandaR": { 10957 "name": "pandaR", 10958 "version": "1.42.0", 10959 "sha256": "031wsqbn8a13cdlfa6139r9s7d8bzvyy7rknaakd5bmrjd6zark5", 10960 "depends": ["Biobase", "BiocGenerics", "RUnit", "ggplot2", "hexbin", "igraph", "matrixStats", "plyr", "reshape"] 10961 }, 10962 "panelcn_mops": { 10963 "name": "panelcn.mops", 10964 "version": "1.32.0", 10965 "sha256": "0dp7apinz8921r7zlwxw5axjxr0v53za04jkqywip2q4wc3y30d1", 10966 "depends": ["GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "cn_mops"] 10967 }, 10968 "panp": { 10969 "name": "panp", 10970 "version": "1.80.0", 10971 "sha256": "0gsikpbsqww8z7zf69cj0s0q2h80yld9455mi5pqm1a6nmylcvnw", 10972 "depends": ["Biobase", "affy"] 10973 }, 10974 "parglms": { 10975 "name": "parglms", 10976 "version": "1.42.0", 10977 "sha256": "0a48b48nw43ydmmfk9rkrmk400gyk6q4rjjnihbbx8gkxzinihld", 10978 "depends": ["BatchJobs", "BiocGenerics", "doParallel", "foreach"] 10979 }, 10980 "parody": { 10981 "name": "parody", 10982 "version": "1.68.0", 10983 "sha256": "0542fwhxjkca8lc5yahmz4fxk571q2vllzlv9rixrnn3v32dphgy", 10984 "depends": [] 10985 }, 10986 "partCNV": { 10987 "name": "partCNV", 10988 "version": "1.8.0", 10989 "sha256": "1z3qzsc5nqp4jnpvhyip7dhknjmlpgalxjaid378j2x62dmg4xcq", 10990 "depends": ["AnnotationHub", "BiocStyle", "GenomicRanges", "Seurat", "SingleCellExperiment", "data_table", "depmixS4", "magrittr"] 10991 }, 10992 "pathMED": { 10993 "name": "pathMED", 10994 "version": "1.2.0", 10995 "sha256": "0z4dd84a3jg17pcr9r6zfdmw7371ypqfm7ppxrcl4qry1cgn49n6", 10996 "depends": ["BiocParallel", "FactoMineR", "GSVA", "caret", "caretEnsemble", "decoupleR", "dplyr", "factoextra", "ggplot2", "magrittr", "matrixStats", "metrica", "pbapply", "reshape2", "singscore", "stringi"] 10997 }, 10998 "pathRender": { 10999 "name": "pathRender", 11000 "version": "1.78.0", 11001 "sha256": "1c2a7m9b0lbglmmk5g6ci0zvc2gc5zaskiaggzgrwjvg7209zhcw", 11002 "depends": ["AnnotationDbi", "RColorBrewer", "Rgraphviz", "cMAP", "graph"] 11003 }, 11004 "pathifier": { 11005 "name": "pathifier", 11006 "version": "1.48.0", 11007 "sha256": "1bkbb7p4dr4ar539h78zxl3l5sz207np48nbjr2vpri7749mi6n7", 11008 "depends": ["R_oo", "princurve"] 11009 }, 11010 "pathlinkR": { 11011 "name": "pathlinkR", 11012 "version": "1.6.0", 11013 "sha256": "1qrm1bkxgyngbqi3i8b8jrlbin431ii0x83448gllnj6mi8yc2w7", 11014 "depends": ["ComplexHeatmap", "circlize", "clusterProfiler", "dplyr", "fgsea", "ggforce", "ggplot2", "ggpubr", "ggraph", "ggrepel", "igraph", "purrr", "sigora", "stringr", "tibble", "tidygraph", "tidyr", "vegan", "visNetwork"] 11015 }, 11016 "pathview": { 11017 "name": "pathview", 11018 "version": "1.50.0", 11019 "sha256": "1cs3nh196wcfphngyx1h0flv0fhydvjyvk1rpq8jc53mcjsdzh5b", 11020 "depends": ["AnnotationDbi", "KEGGREST", "KEGGgraph", "Rgraphviz", "XML", "graph", "org_Hs_eg_db", "png"] 11021 }, 11022 "pathwayPCA": { 11023 "name": "pathwayPCA", 11024 "version": "1.26.0", 11025 "sha256": "0rpak1n9qxwysf5s5hq7b1p41jplljg81k2rzwskfanqyizqib2n", 11026 "depends": ["lars", "survival"] 11027 }, 11028 "pcaExplorer": { 11029 "name": "pcaExplorer", 11030 "version": "3.4.0", 11031 "sha256": "0kaih7vach7a93fl4c5r7fnw3xmdvbwkhlpq31rca6wgsx617964", 11032 "depends": ["AnnotationDbi", "DESeq2", "DT", "GO_db", "GOstats", "GenomicRanges", "IRanges", "NMF", "S4Vectors", "SummarizedExperiment", "base64enc", "biomaRt", "genefilter", "ggplot2", "ggrepel", "heatmaply", "knitr", "limma", "mosdef", "pheatmap", "plotly", "plyr", "rmarkdown", "scales", "shiny", "shinyAce", "shinyBS", "shinydashboard", "threejs", "tidyr", "topGO"] 11033 }, 11034 "pcaMethods": { 11035 "name": "pcaMethods", 11036 "version": "2.2.0", 11037 "sha256": "1ap5czsqg07vj5vy5gmiivpxgdgh14qb0193nxlil0w303a4q37r", 11038 "depends": ["Biobase", "BiocGenerics", "MASS", "Rcpp"] 11039 }, 11040 "pdInfoBuilder": { 11041 "name": "pdInfoBuilder", 11042 "version": "1.74.0", 11043 "sha256": "190cg2c2631v33rckcywryasz7g9kggfba13p9cmi9xbqk3czj3v", 11044 "depends": ["Biobase", "BiocGenerics", "Biostrings", "DBI", "IRanges", "RSQLite", "S4Vectors", "affxparser", "oligo", "oligoClasses"] 11045 }, 11046 "peakCombiner": { 11047 "name": "peakCombiner", 11048 "version": "1.0.0", 11049 "sha256": "0pnv5kx3mcdp6xblpgb6vd34pzf7z3x2ikq10l4cais6df5mzhkk", 11050 "depends": ["GenomicRanges", "IRanges", "Seqinfo", "dplyr", "here", "purrr", "readr", "rlang", "stringr", "tibble", "tidyr", "tidyselect"] 11051 }, 11052 "peakPantheR": { 11053 "name": "peakPantheR", 11054 "version": "1.24.0", 11055 "sha256": "0hgm0zz5m7nkpv7ypxq90dgk0rwm45ija9m3j6gjb2vibzgfxxws", 11056 "depends": ["DT", "MSnbase", "XML", "bslib", "doParallel", "foreach", "ggplot2", "gridExtra", "lubridate", "minpack_lm", "mzR", "pracma", "scales", "shiny", "shinycssloaders", "stringr", "svglite"] 11057 }, 11058 "peco": { 11059 "name": "peco", 11060 "version": "1.22.0", 11061 "sha256": "1jznh029nc8174hrxy3i47q4z4ls16axiif18c0y5hn06yrvcvqa", 11062 "depends": ["SingleCellExperiment", "SummarizedExperiment", "assertthat", "circular", "conicfit", "doParallel", "foreach", "genlasso", "scater"] 11063 }, 11064 "pengls": { 11065 "name": "pengls", 11066 "version": "1.16.0", 11067 "sha256": "1fkg112am6rmn340rmcdc4rxmm7f1zkndszlli3s97p8xh5h9s9k", 11068 "depends": ["BiocParallel", "glmnet", "nlme"] 11069 }, 11070 "pepStat": { 11071 "name": "pepStat", 11072 "version": "1.44.0", 11073 "sha256": "1dnxrhw94sprqjjhbm48gz9amsyis0vsa4m8zv48jv3h4m4rbmz5", 11074 "depends": ["Biobase", "GenomicRanges", "IRanges", "data_table", "fields", "ggplot2", "limma", "plyr"] 11075 }, 11076 "pepXMLTab": { 11077 "name": "pepXMLTab", 11078 "version": "1.44.0", 11079 "sha256": "0vp6ysb86g8760qjnmr7rkf131fga1mm80xkrg6ri3q9r7h85q59", 11080 "depends": ["XML"] 11081 }, 11082 "periodicDNA": { 11083 "name": "periodicDNA", 11084 "version": "1.20.0", 11085 "sha256": "1lqj3bixj6b0xmr1qb4h0myqza1zgqs2wp4fy52vxcraqszg859l", 11086 "depends": ["BSgenome", "BiocParallel", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "cowplot", "ggplot2", "magrittr", "rtracklayer", "zoo"] 11087 }, 11088 "pfamAnalyzeR": { 11089 "name": "pfamAnalyzeR", 11090 "version": "1.10.0", 11091 "sha256": "0cyrhn73hnqq29y2p48bfdrx710yc1m1k9pr83d86y29cz2vz86k", 11092 "depends": ["dplyr", "magrittr", "readr", "stringr", "tibble"] 11093 }, 11094 "pgca": { 11095 "name": "pgca", 11096 "version": "1.34.0", 11097 "sha256": "1p76g6yj0z20rbwcpdzxaahr88aa89ny92hs2rffprrr6l374yl0", 11098 "depends": [] 11099 }, 11100 "pgxRpi": { 11101 "name": "pgxRpi", 11102 "version": "1.6.0", 11103 "sha256": "1mzgyvy16ccn8g5h1i4fcimxg21h5p8a16dxrvgihpdhqrvy0zls", 11104 "depends": ["GenomicRanges", "S4Vectors", "SummarizedExperiment", "attempt", "circlize", "dplyr", "future", "future_apply", "ggplot2", "httr", "lubridate", "survival", "survminer", "yaml"] 11105 }, 11106 "phantasus": { 11107 "name": "phantasus", 11108 "version": "1.29.0", 11109 "sha256": "1nryfgrxzwj90661sfkllq7qcw5svwbs1fiw3bky7rakw7imi2dp", 11110 "depends": ["AnnotationDbi", "Biobase", "DESeq2", "GEOquery", "Matrix", "Rook", "XML", "apeglm", "assertthat", "ccaPP", "config", "curl", "data_table", "edgeR", "fgsea", "fs", "ggplot2", "gtable", "htmltools", "httpuv", "httr", "jsonlite", "limma", "opencpu", "phantasusLite", "pheatmap", "protolite", "rhdf5", "rhdf5client", "scales", "stringr", "svglite", "tidyr", "yaml"] 11111 }, 11112 "phantasusLite": { 11113 "name": "phantasusLite", 11114 "version": "1.8.0", 11115 "sha256": "0fab348czij6snfy99ijjfnk537wpm4p1q0bsrn09hlaazrh3kbi", 11116 "depends": ["Biobase", "data_table", "httr", "rhdf5client", "stringr"] 11117 }, 11118 "phenoTest": { 11119 "name": "phenoTest", 11120 "version": "1.58.0", 11121 "sha256": "0n867ahsz1sqfg5wbn1b50lr02h38bxjywx9a1npxxiwjha3n7n5", 11122 "depends": ["AnnotationDbi", "BMA", "Biobase", "Category", "GSEABase", "Heatplus", "Hmisc", "annotate", "biomaRt", "ellipse", "genefilter", "ggplot2", "gplots", "hgu133a_db", "hopach", "limma", "mgcv", "survival", "xtable"] 11123 }, 11124 "phenomis": { 11125 "name": "phenomis", 11126 "version": "1.12.0", 11127 "sha256": "1sdscv053v7zy1zjw2h39l1rmx0m7crifzx2b4w1gd351qzh8shc", 11128 "depends": ["Biobase", "MultiAssayExperiment", "MultiDataSet", "PMCMRplus", "RColorBrewer", "SummarizedExperiment", "VennDiagram", "biodb", "biodbChebi", "data_table", "futile_logger", "ggplot2", "ggrepel", "htmlwidgets", "igraph", "limma", "plotly", "ranger", "ropls", "tibble", "tidyr"] 11129 }, 11130 "phenopath": { 11131 "name": "phenopath", 11132 "version": "1.34.0", 11133 "sha256": "14n6fm498la467c920qmqxc0scka25zj7939rk91pz1jg9lr93dh", 11134 "depends": ["Rcpp", "SummarizedExperiment", "dplyr", "ggplot2", "tibble", "tidyr"] 11135 }, 11136 "philr": { 11137 "name": "philr", 11138 "version": "1.36.0", 11139 "sha256": "1jvhfz81zyvd6ww57p0hjra43jf3hzpjz9fkxrnqy3i6ngx66a47", 11140 "depends": ["ape", "ggplot2", "ggtree", "phangorn", "tidyr"] 11141 }, 11142 "phosphonormalizer": { 11143 "name": "phosphonormalizer", 11144 "version": "1.34.0", 11145 "sha256": "16lx57gii5mwny2ql08qhxpd3kpbsbzlv122gff7yv3dsxhbirz9", 11146 "depends": ["matrixStats", "plyr"] 11147 }, 11148 "phyloseq": { 11149 "name": "phyloseq", 11150 "version": "1.54.0", 11151 "sha256": "000a4ksians9qxjfcr89qd1h6pr127h2mfjz607sl1h0kml1hiiv", 11152 "depends": ["Biobase", "BiocGenerics", "Biostrings", "ade4", "ape", "biomformat", "cluster", "data_table", "foreach", "ggplot2", "igraph", "multtest", "plyr", "reshape2", "scales", "vegan"] 11153 }, 11154 "piano": { 11155 "name": "piano", 11156 "version": "2.26.0", 11157 "sha256": "0z0dikcqcpd9fw5id4yvgx1kcri3n111zwizrgc80zybcr58s0w2", 11158 "depends": ["Biobase", "BiocGenerics", "DT", "fgsea", "gplots", "htmlwidgets", "igraph", "marray", "relations", "scales", "shiny", "shinydashboard", "shinyjs", "visNetwork"] 11159 }, 11160 "pickgene": { 11161 "name": "pickgene", 11162 "version": "1.82.0", 11163 "sha256": "0ishdijjpww0vhmyi7r1sdyhsqkyv4csj70wz972kg2gwwdw7df5", 11164 "depends": ["MASS"] 11165 }, 11166 "pipeComp": { 11167 "name": "pipeComp", 11168 "version": "1.20.0", 11169 "sha256": "12rzvmikam9rcy30739689xgizhli94mzv596gcbki9xax5s9h7y", 11170 "depends": ["BiocParallel", "ComplexHeatmap", "Matrix", "RColorBrewer", "Rtsne", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "aricode", "circlize", "clue", "cluster", "cowplot", "dplyr", "ggplot2", "intrinsicDimension", "knitr", "matrixStats", "randomcoloR", "reshape2", "scales", "scater", "scran", "uwot", "viridisLite"] 11171 }, 11172 "pipeFrame": { 11173 "name": "pipeFrame", 11174 "version": "1.26.0", 11175 "sha256": "0rg01a3jprmicj6wqbvysdwgsmjmhnbfbsmhblbr5spzbci17lm1", 11176 "depends": ["BSgenome", "Biostrings", "Seqinfo", "digest", "magrittr", "rmarkdown", "visNetwork"] 11177 }, 11178 "planet": { 11179 "name": "planet", 11180 "version": "1.18.0", 11181 "sha256": "0wzmbip9abl6ism4504c01nv57sjm4g7rl25zk8g7vjllvry67lb", 11182 "depends": ["dplyr", "magrittr", "tibble"] 11183 }, 11184 "planttfhunter": { 11185 "name": "planttfhunter", 11186 "version": "1.10.0", 11187 "sha256": "0has9lyfn3vxlwhw62c1fwdpqdczvchi2z8qm01v5jvmmk88lgfh", 11188 "depends": ["Biostrings", "SummarizedExperiment"] 11189 }, 11190 "plasmut": { 11191 "name": "plasmut", 11192 "version": "1.8.0", 11193 "sha256": "01f7kzid0b8qaw73gcsljlr2mw2gmdvg9pmv6qcyq7vprch2xsf0", 11194 "depends": ["dplyr", "tibble"] 11195 }, 11196 "plgem": { 11197 "name": "plgem", 11198 "version": "1.82.0", 11199 "sha256": "00y34si5xcp7va8paxqfg6hbd6f4s8r6myrz0rh2280173nwyfz3", 11200 "depends": ["Biobase", "MASS"] 11201 }, 11202 "plier": { 11203 "name": "plier", 11204 "version": "1.80.0", 11205 "sha256": "16b31r42lgna7yk692ann6p16n446qjl5aph83v4cjwgrnqvj42z", 11206 "depends": ["Biobase", "affy"] 11207 }, 11208 "plotGrouper": { 11209 "name": "plotGrouper", 11210 "version": "1.28.0", 11211 "sha256": "1s7n1rwl736hx1awjh39dgb4z3rllkbm3xxmrs74v4ibxphlccv0", 11212 "depends": ["Hmisc", "colourpicker", "dplyr", "egg", "ggplot2", "ggpubr", "gridExtra", "gtable", "magrittr", "readr", "readxl", "rlang", "scales", "shiny", "shinythemes", "stringr", "tibble", "tidyr"] 11213 }, 11214 "plotgardener": { 11215 "name": "plotgardener", 11216 "version": "1.16.0", 11217 "sha256": "1cbxmk2imna9gw3khzzjzhfa75sanqx7hhw0qzhhh2f0szj8z1s3", 11218 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rcpp", "curl", "data_table", "dplyr", "ggplotify", "glue", "plyranges", "purrr", "rhdf5", "rlang", "strawr", "withr"] 11219 }, 11220 "plyinteractions": { 11221 "name": "plyinteractions", 11222 "version": "1.8.0", 11223 "sha256": "1k5vvja82dyyfl8fidybxmm81q69y636dfl9pcb7mljp8b97b9k7", 11224 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "Seqinfo", "dplyr", "plyranges", "rlang", "tibble", "tidyselect"] 11225 }, 11226 "plyranges": { 11227 "name": "plyranges", 11228 "version": "1.30.0", 11229 "sha256": "0ci212srw0pkps3xvnx92qvxnmvf897wvik9x18wkxh07k5b45r8", 11230 "depends": ["BiocGenerics", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "dplyr", "magrittr", "rlang", "rtracklayer", "tidyselect"] 11231 }, 11232 "plyxp": { 11233 "name": "plyxp", 11234 "version": "1.4.0", 11235 "sha256": "1gl95ck1hmffbfvhkl0kvhmk3nnvg7qjkn9knxvjwhyl3qbl1iyw", 11236 "depends": ["S4Vectors", "S7", "SummarizedExperiment", "cli", "dplyr", "glue", "pillar", "purrr", "rlang", "tibble", "tidyr", "tidyselect", "vctrs"] 11237 }, 11238 "pmm": { 11239 "name": "pmm", 11240 "version": "1.42.0", 11241 "sha256": "0py4aw2p37h3nq87g1fwjx342g89wbv0z8kvxj74ljkyjrdi9cbh", 11242 "depends": ["lme4"] 11243 }, 11244 "pmp": { 11245 "name": "pmp", 11246 "version": "1.21.0", 11247 "sha256": "1dprxhggfdxcrj2s3fwhlhi6abppkvi63f2mxgjmfxflj2x9zjjp", 11248 "depends": ["S4Vectors", "SummarizedExperiment", "ggplot2", "impute", "matrixStats", "missForest", "pcaMethods", "reshape2"] 11249 }, 11250 "podkat": { 11251 "name": "podkat", 11252 "version": "1.42.0", 11253 "sha256": "04438ik0sivkql3vj9jfjfqrwp3i6a7knp0ciqhrf6ij7da9j57c", 11254 "depends": ["BSgenome", "Biobase", "BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "Rhtslib", "Rsamtools", "Seqinfo"] 11255 }, 11256 "poem": { 11257 "name": "poem", 11258 "version": "1.2.0", 11259 "sha256": "1i13vcz0y32j8i1ljir5r8py6kz5vmdih8v4ykxmr0mbabh4rc5p", 11260 "depends": ["BiocNeighbors", "BiocParallel", "Matrix", "SpatialExperiment", "SummarizedExperiment", "aricode", "bluster", "clevr", "clue", "cluster", "elsa", "fclust", "igraph", "matrixStats", "mclustcomp", "pdist", "sp", "spdep"] 11261 }, 11262 "pogos": { 11263 "name": "pogos", 11264 "version": "1.30.0", 11265 "sha256": "1g7xbq2a195v7r33psshq8080hfh2kn2daa78665mn16k6kmchzb", 11266 "depends": ["S4Vectors", "ggplot2", "httr", "ontoProc", "rjson", "shiny"] 11267 }, 11268 "powerTCR": { 11269 "name": "powerTCR", 11270 "version": "1.30.0", 11271 "sha256": "1j7c8cg5zv1d1p1rjw1f1ai75023gd3lz5cyyj5a0r7kgblpdnfd", 11272 "depends": ["VGAM", "cubature", "doParallel", "evmix", "foreach", "magrittr", "purrr", "truncdist", "vegan"] 11273 }, 11274 "ppcseq": { 11275 "name": "ppcseq", 11276 "version": "1.18.0", 11277 "sha256": "1j5jp7g9q4l89abivhsdjvi18sy7fx4axqf2rp3mppnhfqjcnkfg", 11278 "depends": ["BH", "Rcpp", "RcppEigen", "RcppParallel", "StanHeaders", "benchmarkme", "dplyr", "edgeR", "foreach", "ggplot2", "lifecycle", "magrittr", "purrr", "rlang", "rstan", "rstantools", "tibble", "tidybayes", "tidyr"] 11279 }, 11280 "pqsfinder": { 11281 "name": "pqsfinder", 11282 "version": "2.26.0", 11283 "sha256": "0giy76czahjvafvvylg619dc1wk50svjrhmxa1gmbb8hxa8ajf0z", 11284 "depends": ["BH", "Biostrings", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors"] 11285 }, 11286 "pram": { 11287 "name": "pram", 11288 "version": "1.26.0", 11289 "sha256": "0h9335p8b2g4g94yf17jp66swl74l5sf9f82y8jrw0flhw7qwsgw", 11290 "depends": ["BiocGenerics", "BiocParallel", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "data_table", "rtracklayer"] 11291 }, 11292 "prebs": { 11293 "name": "prebs", 11294 "version": "1.50.0", 11295 "sha256": "0wi5s05mhs0gw53vrqv1m54d01p1wf7b723zj6all5108482l0fc", 11296 "depends": ["Biobase", "GenomicAlignments", "GenomicRanges", "IRanges", "RPA", "S4Vectors", "Seqinfo", "affy"] 11297 }, 11298 "preciseTAD": { 11299 "name": "preciseTAD", 11300 "version": "1.20.0", 11301 "sha256": "0q6a0w6la5799mhr8isdqqsk83bkr7d6yaqnhd8fbk0grwgnrbfs", 11302 "depends": ["GenomicRanges", "IRanges", "ModelMetrics", "PRROC", "S4Vectors", "caret", "cluster", "dbscan", "doSNOW", "e1071", "foreach", "gtools", "pROC", "pbapply", "rCGH", "randomForest"] 11303 }, 11304 "preprocessCore": { 11305 "name": "preprocessCore", 11306 "version": "1.72.0", 11307 "sha256": "0kc8af6kcp10iassdfxlx5nj63837dgv2gi23pwznz0lf4ihawj4", 11308 "depends": [] 11309 }, 11310 "primirTSS": { 11311 "name": "primirTSS", 11312 "version": "1.28.0", 11313 "sha256": "1s3kkx5ykgx8lf075hf581w84g9i0gvp0qhz9l31pvr6h2fgq5cx", 11314 "depends": ["BSgenome_Hsapiens_UCSC_hg38", "BiocGenerics", "Biostrings", "GenomicRanges", "GenomicScores", "Gviz", "IRanges", "JASPAR2018", "R_utils", "S4Vectors", "TFBSTools", "dplyr", "phastCons100way_UCSC_hg38", "purrr", "rtracklayer", "shiny", "stringr", "tibble", "tidyr"] 11315 }, 11316 "proActiv": { 11317 "name": "proActiv", 11318 "version": "1.20.0", 11319 "sha256": "1p9wzwv1i4zps487g2vazxbw3p12vsr14ipmjk34ab3wh8bx3iqy", 11320 "depends": ["AnnotationDbi", "BiocParallel", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "ggplot2", "gplots", "rlang", "scales", "tibble", "txdbmaker"] 11321 }, 11322 "proBAMr": { 11323 "name": "proBAMr", 11324 "version": "1.44.0", 11325 "sha256": "0j9znhzrbv0xi78lpjs9fa98f0g3j8hsy01fx1r0kadbdblnlngy", 11326 "depends": ["AnnotationDbi", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "rtracklayer", "txdbmaker"] 11327 }, 11328 "proDA": { 11329 "name": "proDA", 11330 "version": "1.24.0", 11331 "sha256": "1f67rsnmc71nsza73aw9v6x9lkpbgsz0h8gkyy7ay61dqlfmpd17", 11332 "depends": ["BiocGenerics", "S4Vectors", "SummarizedExperiment", "extraDistr"] 11333 }, 11334 "procoil": { 11335 "name": "procoil", 11336 "version": "2.38.0", 11337 "sha256": "08a0r51zwnapdn6l3arlaiq23qhwa93mj5s1jakssfn85if68fxl", 11338 "depends": ["Biostrings", "S4Vectors", "kebabs"] 11339 }, 11340 "profileScoreDist": { 11341 "name": "profileScoreDist", 11342 "version": "1.38.0", 11343 "sha256": "1md6hgyc5mlcgjqh51wk1g0n0zrdr1mcqn27y8kagmrvz04js383", 11344 "depends": ["BiocGenerics", "Rcpp"] 11345 }, 11346 "progeny": { 11347 "name": "progeny", 11348 "version": "1.32.0", 11349 "sha256": "0hlibwsk7b15n83qpwlk5ahlrqvi8qvwahwv5bs8ydkfkgaywhr4", 11350 "depends": ["Biobase", "decoupleR", "dplyr", "ggplot2", "ggrepel", "gridExtra", "reshape2", "tidyr"] 11351 }, 11352 "projectR": { 11353 "name": "projectR", 11354 "version": "1.26.0", 11355 "sha256": "1lh43myc9z3cdg1anm2wdm3h0188kvaf7ihy0h35kd3qj6icr018", 11356 "depends": ["Matrix", "MatrixModels", "NMF", "RColorBrewer", "ROCR", "SingleCellExperiment", "cluster", "cowplot", "dplyr", "fgsea", "ggalluvial", "ggplot2", "ggrepel", "limma", "msigdbr", "reshape2", "scales", "tsne", "umap", "viridis"] 11357 }, 11358 "protGear": { 11359 "name": "protGear", 11360 "version": "1.14.0", 11361 "sha256": "086k582c3npqmcj8j2fdyc3x80cdfd9ywl5r9yaig7ss86h9p7fm", 11362 "depends": ["Biobase", "FactoMineR", "GGally", "Kendall", "MASS", "data_table", "dplyr", "factoextra", "flexdashboard", "genefilter", "ggplot2", "ggpubr", "gtools", "htmltools", "knitr", "limma", "magrittr", "pheatmap", "plotly", "plyr", "purrr", "readr", "remotes", "rlang", "rmarkdown", "shiny", "shinydashboard", "styler", "tibble", "tidyr", "vsn"] 11363 }, 11364 "proteinProfiles": { 11365 "name": "proteinProfiles", 11366 "version": "1.50.0", 11367 "sha256": "0ddzzap6wglf8fi1d916i2nfqryrifg7gg24xlr8slwj5c99k065", 11368 "depends": [] 11369 }, 11370 "psichomics": { 11371 "name": "psichomics", 11372 "version": "1.36.0", 11373 "sha256": "1f20ldcjlbj0r07xq4pxny7bnmx74pmc9y72gkp1n639f179n5vw", 11374 "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "DT", "R_utils", "Rcpp", "Rfast", "SummarizedExperiment", "XML", "cluster", "colourpicker", "data_table", "digest", "dplyr", "edgeR", "fastICA", "fastmatch", "ggplot2", "ggrepel", "highcharter", "htmltools", "httr", "jsonlite", "limma", "pairsD3", "plyr", "purrr", "recount", "reshape2", "shiny", "shinyBS", "shinyjs", "stringr", "survival", "xtable"] 11375 }, 11376 "ptairMS": { 11377 "name": "ptairMS", 11378 "version": "1.18.0", 11379 "sha256": "0cxachz3wpnq8g641f24ghgy0byr3dfy1izagg754i4sdlq2097q", 11380 "depends": ["Biobase", "DT", "Hmisc", "MSnbase", "Rcpp", "bit64", "chron", "data_table", "doParallel", "enviPat", "foreach", "ggplot2", "ggpubr", "gridExtra", "minpack_lm", "plotly", "rhdf5", "rlang", "scales", "shiny", "shinyscreenshot", "signal"] 11381 }, 11382 "puma": { 11383 "name": "puma", 11384 "version": "3.52.0", 11385 "sha256": "00c2h2bzlpxc7hg04dn1vikydhfdfc86f55qdv73y96cpk6sa0c7", 11386 "depends": ["Biobase", "affy", "affyio", "mclust", "oligo", "oligoClasses"] 11387 }, 11388 "pvac": { 11389 "name": "pvac", 11390 "version": "1.58.0", 11391 "sha256": "0x46n6f96k7ifn29sl6k4aassin42897dhjd1nr0gpiwpgvrsygd", 11392 "depends": ["Biobase", "affy"] 11393 }, 11394 "pvca": { 11395 "name": "pvca", 11396 "version": "1.50.0", 11397 "sha256": "0bh1snrzx1p73b3xn1ddqpvqr1s3rycb0ffhlwpdxrmf3d7ykcgp", 11398 "depends": ["Biobase", "Matrix", "lme4", "vsn"] 11399 }, 11400 "pwalign": { 11401 "name": "pwalign", 11402 "version": "1.6.0", 11403 "sha256": "1f5py5xip1nd2qpa9fhfkxz9sznq8j3pcjpcaq8pydz7psy2jpin", 11404 "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors", "XVector"] 11405 }, 11406 "qPLEXanalyzer": { 11407 "name": "qPLEXanalyzer", 11408 "version": "1.27.0", 11409 "sha256": "0xbb933yhfbmgibjzic342rci3sw9dwxgz5wxgxfmzqwyivjp3px", 11410 "depends": ["Biobase", "BiocGenerics", "Biostrings", "IRanges", "MSnbase", "RColorBrewer", "assertthat", "dplyr", "ggdendro", "ggplot2", "limma", "magrittr", "preprocessCore", "purrr", "readr", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect"] 11411 }, 11412 "qcmetrics": { 11413 "name": "qcmetrics", 11414 "version": "1.48.0", 11415 "sha256": "1si14qxh8ki0ihjfvyjr4kxi1iqcbb48g0q50i7hnq6aydfc18qw", 11416 "depends": ["Biobase", "S4Vectors", "knitr", "pander", "xtable"] 11417 }, 11418 "qmtools": { 11419 "name": "qmtools", 11420 "version": "1.14.0", 11421 "sha256": "06kpza9mrmkhpwsr7d8mwr1pflmq4hirgbgywqqjp0pp7r0ykq2g", 11422 "depends": ["MsCoreUtils", "SummarizedExperiment", "VIM", "ggplot2", "heatmaply", "igraph", "limma", "patchwork", "rlang", "scales"] 11423 }, 11424 "qpcrNorm": { 11425 "name": "qpcrNorm", 11426 "version": "1.68.0", 11427 "sha256": "1zs7zfjv8nck70wfb62ypcwpx0m3i7m9gcanswphjf7rhhdnwlr1", 11428 "depends": ["Biobase", "affy", "limma"] 11429 }, 11430 "qpgraph": { 11431 "name": "qpgraph", 11432 "version": "2.44.0", 11433 "sha256": "0qb4jczksj174wzfvzdhyj1bv4ijmhi25zdhshf54sp62jg02n10", 11434 "depends": ["AnnotationDbi", "Biobase", "BiocParallel", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rgraphviz", "S4Vectors", "Seqinfo", "annotate", "graph", "mvtnorm", "qtl"] 11435 }, 11436 "qsea": { 11437 "name": "qsea", 11438 "version": "1.36.0", 11439 "sha256": "1a7454b73idzpz406wqcqkspl8vvs60gz4fq6apvqhb9xmgsyzq4", 11440 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicRanges", "HMMcopy", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "gtools", "limma", "rtracklayer", "zoo"] 11441 }, 11442 "qsmooth": { 11443 "name": "qsmooth", 11444 "version": "1.26.0", 11445 "sha256": "0fgb1jj8wha5q9zdwh09q4xlr9m1pga0c38gq8zx4mg38ik6siwv", 11446 "depends": ["Hmisc", "SummarizedExperiment", "sva"] 11447 }, 11448 "qsvaR": { 11449 "name": "qsvaR", 11450 "version": "1.14.0", 11451 "sha256": "12mrzjpydy767skp2664z5iw7zyi28rjlwp8d4s5php0fm5aw9gb", 11452 "depends": ["SummarizedExperiment", "dplyr", "ggplot2", "rlang", "sva"] 11453 }, 11454 "quantiseqr": { 11455 "name": "quantiseqr", 11456 "version": "1.18.0", 11457 "sha256": "0s6x3pg7mx89y6bnzzak8qw82yxkw74zpj5lgqimkmvh9f0gf35c", 11458 "depends": ["Biobase", "MASS", "SummarizedExperiment", "ggplot2", "limSolve", "preprocessCore", "rlang", "tidyr"] 11459 }, 11460 "quantro": { 11461 "name": "quantro", 11462 "version": "1.44.0", 11463 "sha256": "1g2wzbivpj6vqlh1hy2g468y6r9lbkv6007k6fqvvm2gh4b1xac4", 11464 "depends": ["Biobase", "RColorBrewer", "doParallel", "foreach", "ggplot2", "iterators", "minfi"] 11465 }, 11466 "quantsmooth": { 11467 "name": "quantsmooth", 11468 "version": "1.76.0", 11469 "sha256": "1cny9al0cb1z2n2zr4lr8yj3ghrkp35x5glkzkl2lkbrn53ij7l5", 11470 "depends": ["quantreg"] 11471 }, 11472 "qusage": { 11473 "name": "qusage", 11474 "version": "2.44.0", 11475 "sha256": "17i0fr1y1n1ygml2x1i1rabhzcci741ld91qrdvn2q34z1jvnqb0", 11476 "depends": ["Biobase", "emmeans", "fftw", "limma", "nlme"] 11477 }, 11478 "qvalue": { 11479 "name": "qvalue", 11480 "version": "2.42.0", 11481 "sha256": "1wv57xrls786m26316k5i9innk4hgpdfz9hrj8akvavnqrc5myif", 11482 "depends": ["ggplot2", "reshape2"] 11483 }, 11484 "r3Cseq": { 11485 "name": "r3Cseq", 11486 "version": "1.56.0", 11487 "sha256": "0h6viyf8g6bgx14y25i8s1xx8jh5dx4lh5ddfq566zp3y93wp78c", 11488 "depends": ["Biostrings", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "Seqinfo", "VGAM", "data_table", "qvalue", "rtracklayer", "sqldf"] 11489 }, 11490 "rBLAST": { 11491 "name": "rBLAST", 11492 "version": "1.6.0", 11493 "sha256": "1kk10kb521rqsb4557h55qj5z6yv2nmkrz160r78lscdgx72z42p", 11494 "depends": ["BiocFileCache", "Biostrings"] 11495 }, 11496 "rBiopaxParser": { 11497 "name": "rBiopaxParser", 11498 "version": "2.50.0", 11499 "sha256": "1lc8ib9gyfsbswm8qv719qw7fj7h5pwy1qqg616ykabqfg08iczs", 11500 "depends": ["XML", "data_table"] 11501 }, 11502 "rCGH": { 11503 "name": "rCGH", 11504 "version": "1.40.0", 11505 "sha256": "0s4manwnal628ffw3l4mv1qzpsrk31h3k85wx258k656000nm5dv", 11506 "depends": ["AnnotationDbi", "DNAcopy", "GenomicFeatures", "GenomicRanges", "IRanges", "Seqinfo", "TxDb_Hsapiens_UCSC_hg18_knownGene", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "aCGH", "affy", "ggplot2", "lattice", "limma", "mclust", "org_Hs_eg_db", "plyr", "shiny"] 11507 }, 11508 "rGREAT": { 11509 "name": "rGREAT", 11510 "version": "2.11.0", 11511 "sha256": "1ciz4cn04vm9sniblf4adkgkcldsjnfzssv441madl364da6m9jq", 11512 "depends": ["AnnotationDbi", "DT", "GO_db", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "GetoptLong", "GlobalOptions", "IRanges", "RColorBrewer", "RCurl", "Rcpp", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "circlize", "digest", "doParallel", "foreach", "org_Hs_eg_db", "progress", "rjson", "shiny"] 11513 }, 11514 "rGenomeTracks": { 11515 "name": "rGenomeTracks", 11516 "version": "1.16.0", 11517 "sha256": "11sy8lx3pzp6k2fpidhrwd0q9qqq5ys814rlz4vbdwv0d0ymxfbl", 11518 "depends": ["imager", "rGenomeTracksData", "reticulate"] 11519 }, 11520 "rRDP": { 11521 "name": "rRDP", 11522 "version": "1.44.0", 11523 "sha256": "1xsnd1pjijxdiyqh677zsmd2k6ycyfvmxlvbr1sd2sags7dpqlh4", 11524 "depends": ["Biostrings", "rJava"] 11525 }, 11526 "rSWeeP": { 11527 "name": "rSWeeP", 11528 "version": "1.22.0", 11529 "sha256": "13vhig0c8h6irczcc7ckv1pxj2pf27a6bcbpgskm25wh1lcmaqii", 11530 "depends": ["Biostrings", "doParallel", "foreach", "stringi"] 11531 }, 11532 "rScudo": { 11533 "name": "rScudo", 11534 "version": "1.26.0", 11535 "sha256": "12xx48ng75j1n6qlmfvdy0cv5nrlrlpm0g0ggqw1v51a2ka8jalv", 11536 "depends": ["Biobase", "BiocGenerics", "S4Vectors", "SummarizedExperiment", "igraph", "stringr"] 11537 }, 11538 "rTRM": { 11539 "name": "rTRM", 11540 "version": "1.48.0", 11541 "sha256": "1s3ql1byahy4b9wsf3511268v4innk5fj5d6cggbw0880529jkgy", 11542 "depends": ["AnnotationDbi", "DBI", "RSQLite", "igraph"] 11543 }, 11544 "rTRMui": { 11545 "name": "rTRMui", 11546 "version": "1.48.0", 11547 "sha256": "0qa7j53xr22jp6s11piny5kscjnd328s4b9irg4ribw1jzpcfacx", 11548 "depends": ["MotifDb", "org_Hs_eg_db", "org_Mm_eg_db", "rTRM", "shiny"] 11549 }, 11550 "rWikiPathways": { 11551 "name": "rWikiPathways", 11552 "version": "1.30.0", 11553 "sha256": "06rgqn8a0qww4lcxix0967i2vks6smddgys26ymhrdjqikx53cjf", 11554 "depends": ["RCurl", "XML", "data_table", "dplyr", "httr", "lubridate", "purrr", "readr", "rjson", "stringr", "tidyr"] 11555 }, 11556 "raer": { 11557 "name": "raer", 11558 "version": "1.8.0", 11559 "sha256": "0pnpi7m3vrqpgv1d7dpzvvh9a46nlx70qjjnf5yif05lfh44nbkq", 11560 "depends": ["BSgenome", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "Rhtslib", "Rsamtools", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SummarizedExperiment", "cli", "rtracklayer"] 11561 }, 11562 "rain": { 11563 "name": "rain", 11564 "version": "1.44.0", 11565 "sha256": "0iksgh33bavhpgzavf9qw9x15yyhphm9hnfyz0lyghcd5mszhw4i", 11566 "depends": ["gmp", "multtest"] 11567 }, 11568 "ramr": { 11569 "name": "ramr", 11570 "version": "1.18.0", 11571 "sha256": "00k92aa08gpvgclghx1nsxf6qw4iks3fgpplgg6dpys1q9mg018g", 11572 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors", "Seqinfo", "data_table"] 11573 }, 11574 "ramwas": { 11575 "name": "ramwas", 11576 "version": "1.34.0", 11577 "sha256": "0m56jj1fn7czvqm8w79m11rs2w7xblpflw5sjnxmn8zxx5nw5m14", 11578 "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "KernSmooth", "Rsamtools", "biomaRt", "digest", "filematrix", "glmnet"] 11579 }, 11580 "randPack": { 11581 "name": "randPack", 11582 "version": "1.56.0", 11583 "sha256": "1gxmy6mlgbmz290fnw7b6l1fq1qvwim77jmk02wnlg09qafbprmj", 11584 "depends": ["Biobase"] 11585 }, 11586 "randRotation": { 11587 "name": "randRotation", 11588 "version": "1.22.0", 11589 "sha256": "06fwdzmpyifv1mdq157h2gh6qdyqx0gxhfra7b52sfz7pj4yh47d", 11590 "depends": ["Rdpack"] 11591 }, 11592 "rawDiag": { 11593 "name": "rawDiag", 11594 "version": "1.6.0", 11595 "sha256": "0h73k31j6fffs1nbf2r0190krscm9rxawib9cnbakfagp2qfqywf", 11596 "depends": ["BiocManager", "BiocParallel", "dplyr", "ggplot2", "hexbin", "htmltools", "rawrr", "reshape2", "rlang", "scales", "shiny"] 11597 }, 11598 "rawrr": { 11599 "name": "rawrr", 11600 "version": "1.18.0", 11601 "sha256": "1cwf1k837x3j36iqvrvff9wb19y6nyq6015va3rnd7ipfavjjgk1", 11602 "depends": [] 11603 }, 11604 "rbsurv": { 11605 "name": "rbsurv", 11606 "version": "2.68.0", 11607 "sha256": "0bmb31b7l6x4rnlxzqla8pi2wgp5gn96lls3jr9nrvvv5camiq9p", 11608 "depends": ["Biobase", "survival"] 11609 }, 11610 "rcellminer": { 11611 "name": "rcellminer", 11612 "version": "2.32.0", 11613 "sha256": "16ma34rxz5lmk2p42glq53z4vv0c5rk3lq4wl01hg2pc15yx3rbq", 11614 "depends": ["Biobase", "ggplot2", "gplots", "rcellminerData", "shiny", "stringr"] 11615 }, 11616 "rebook": { 11617 "name": "rebook", 11618 "version": "1.20.0", 11619 "sha256": "0f5i3s9s0br0zgg8dw8hqzg6ddgwcaflaxc0j8k5krfma3np83c9", 11620 "depends": ["BiocStyle", "CodeDepends", "dir_expiry", "filelock", "knitr", "rmarkdown"] 11621 }, 11622 "reconsi": { 11623 "name": "reconsi", 11624 "version": "1.22.0", 11625 "sha256": "164nzs7jcrq149w4gdji4g7d9mvzadbab0qgq62a2ylk275kfa75", 11626 "depends": ["Matrix", "ggplot2", "ks", "matrixStats", "phyloseq", "reshape2"] 11627 }, 11628 "recount": { 11629 "name": "recount", 11630 "version": "1.36.0", 11631 "sha256": "16n2wsxl857v25wzzy0v0j1sycm7a1wcg07qdxnfp9nf53fn2v2l", 11632 "depends": ["BiocParallel", "GEOquery", "GenomeInfoDb", "GenomicRanges", "IRanges", "RCurl", "S4Vectors", "SummarizedExperiment", "derfinder", "downloader", "rentrez", "rtracklayer"] 11633 }, 11634 "recount3": { 11635 "name": "recount3", 11636 "version": "1.20.0", 11637 "sha256": "1j7dir2bqv813ridsa2ka5dwf2zmd8fxx1s385rlbchw09rgy461", 11638 "depends": ["BiocFileCache", "GenomicRanges", "Matrix", "R_utils", "S4Vectors", "SummarizedExperiment", "data_table", "httr", "rtracklayer", "sessioninfo"] 11639 }, 11640 "recountmethylation": { 11641 "name": "recountmethylation", 11642 "version": "1.20.0", 11643 "sha256": "0nlhaxiyfh0mx7ygi99a1gz5mm7qrdx7y0x2gncal19fpbb3rd8v", 11644 "depends": ["BiocFileCache", "DelayedMatrixStats", "HDF5Array", "RCurl", "R_utils", "S4Vectors", "basilisk", "minfi", "reticulate", "rhdf5"] 11645 }, 11646 "recoup": { 11647 "name": "recoup", 11648 "version": "1.38.0", 11649 "sha256": "0dl1vagixfqlggdnq8ijj0bi3xrm80rv8d48d317i5l325zqk7c6", 11650 "depends": ["BiocGenerics", "Biostrings", "ComplexHeatmap", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "Rsamtools", "S4Vectors", "Seqinfo", "biomaRt", "circlize", "ggplot2", "httr", "rtracklayer", "stringr", "txdbmaker"] 11651 }, 11652 "regionReport": { 11653 "name": "regionReport", 11654 "version": "1.44.0", 11655 "sha256": "0pa23vwjmn56ln35g38y16ayxmywh2q0jp9pb819favc8plypji8", 11656 "depends": ["BiocStyle", "DEFormats", "DESeq2", "GenomeInfoDb", "GenomicRanges", "RefManageR", "S4Vectors", "Seqinfo", "SummarizedExperiment", "derfinder", "knitr", "knitrBootstrap", "rmarkdown"] 11657 }, 11658 "regioneR": { 11659 "name": "regioneR", 11660 "version": "1.42.0", 11661 "sha256": "1s96qn8b4g4bk52d2jpyk1m4nw87ay2zhy6xf4scaqs4gd227196", 11662 "depends": ["BSgenome", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "memoise", "rtracklayer"] 11663 }, 11664 "regioneReloaded": { 11665 "name": "regioneReloaded", 11666 "version": "1.12.0", 11667 "sha256": "02ycyzhprcijv891cscgssknaqnrfch3wgdc9v1ypg0lyfsqan8y", 11668 "depends": ["RColorBrewer", "Rtsne", "cluster", "ggplot2", "ggrepel", "regioneR", "reshape2", "scales", "umap"] 11669 }, 11670 "regsplice": { 11671 "name": "regsplice", 11672 "version": "1.36.0", 11673 "sha256": "0rghn9as68m6mr2d0ra0dk99y73icjnzx80mmkckw01y9z34dm42", 11674 "depends": ["S4Vectors", "SummarizedExperiment", "edgeR", "glmnet", "limma", "pbapply"] 11675 }, 11676 "regutools": { 11677 "name": "regutools", 11678 "version": "1.22.0", 11679 "sha256": "1pf8ljrcjj9d8jnayslbl4br90szc453c4lmnhf56vfg62s2qbjw", 11680 "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "Biostrings", "DBI", "GenomicRanges", "Gviz", "IRanges", "RCy3", "RSQLite", "S4Vectors"] 11681 }, 11682 "retrofit": { 11683 "name": "retrofit", 11684 "version": "1.10.0", 11685 "sha256": "00aax7vq90c9jsisar7siqrj0n498jzrhl2ja4xkx19d4jh3bzcy", 11686 "depends": ["Rcpp"] 11687 }, 11688 "rexposome": { 11689 "name": "rexposome", 11690 "version": "1.32.0", 11691 "sha256": "00x020bjh7f4pma304i65c6l9wpbqgqkvsfb9yaanaj9sph33q8l", 11692 "depends": ["Biobase", "FactoMineR", "Hmisc", "S4Vectors", "circlize", "corrplot", "ggplot2", "ggrepel", "ggridges", "glmnet", "gplots", "gridExtra", "gtools", "imputeLCMD", "lme4", "lsr", "mice", "pryr", "reshape2", "scales", "scatterplot3d", "stringr"] 11693 }, 11694 "rfPred": { 11695 "name": "rfPred", 11696 "version": "1.48.0", 11697 "sha256": "016gq8lbcixpa0xgq054vg20v1qaklls765aq9nfrcnkgk9ygday", 11698 "depends": ["GenomicRanges", "IRanges", "Rsamtools", "Seqinfo", "data_table"] 11699 }, 11700 "rfaRm": { 11701 "name": "rfaRm", 11702 "version": "1.22.0", 11703 "sha256": "1xpjy9zxyk0qd50sk5rq1l7zxabjgvd1vx04qms43q5fqk5bq2qg", 11704 "depends": ["Biostrings", "IRanges", "S4Vectors", "data_table", "httr", "jsonlite", "magick", "rsvg", "rvest", "stringi", "xml2"] 11705 }, 11706 "rgoslin": { 11707 "name": "rgoslin", 11708 "version": "1.14.0", 11709 "sha256": "05dazq764zksnlb6ymiiz18dz9m8b30kqigwcs16svg1nfzjyav3", 11710 "depends": ["Rcpp", "dplyr"] 11711 }, 11712 "rgsepd": { 11713 "name": "rgsepd", 11714 "version": "1.42.0", 11715 "sha256": "0zswyh9c3ak9zsd0zkzx8ca22a56a6zc2p65zihva3lvhm4wv7z0", 11716 "depends": ["AnnotationDbi", "DESeq2", "GO_db", "SummarizedExperiment", "biomaRt", "goseq", "gplots", "org_Hs_eg_db"] 11717 }, 11718 "rhdf5": { 11719 "name": "rhdf5", 11720 "version": "2.54.0", 11721 "sha256": "1psfaqha2sflpp0sm0j3wcxscxb9490pbck69izrsfrrg75jbf7n", 11722 "depends": ["Rhdf5lib", "rhdf5filters"] 11723 }, 11724 "rhdf5client": { 11725 "name": "rhdf5client", 11726 "version": "1.32.0", 11727 "sha256": "04h3ff62j8ci0ffrpj4rkhdfdqgi201q5dd9qfbvqvqfk24vs8mw", 11728 "depends": ["DelayedArray", "data_table", "httr", "rjson"] 11729 }, 11730 "rhdf5filters": { 11731 "name": "rhdf5filters", 11732 "version": "1.22.0", 11733 "sha256": "0idr4l0byd039hdw74zq3ay9yjy6dd579l68r8bfh1q2884y2zsz", 11734 "depends": ["Rhdf5lib"] 11735 }, 11736 "rhinotypeR": { 11737 "name": "rhinotypeR", 11738 "version": "1.4.0", 11739 "sha256": "0sp24s5l95bv7dayx6y5f3b8vinv4l4bzk5a556f3i62l5p49yvn", 11740 "depends": ["Biostrings", "MSA2dist", "msa"] 11741 }, 11742 "riboSeqR": { 11743 "name": "riboSeqR", 11744 "version": "1.44.0", 11745 "sha256": "02njg9qxghln611ax5m98hq2xidka6ppy3ywx8171cz7cx1mqymv", 11746 "depends": ["GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "abind", "baySeq", "seqLogo"] 11747 }, 11748 "ribor": { 11749 "name": "ribor", 11750 "version": "1.22.0", 11751 "sha256": "04zaghm2b2g9m7wjsirm0dfx75cqgbxg6nrkravq8p8zm11w8070", 11752 "depends": ["S4Vectors", "dplyr", "ggplot2", "hash", "rhdf5", "rlang", "tidyr", "yaml"] 11753 }, 11754 "ribosomeProfilingQC": { 11755 "name": "ribosomeProfilingQC", 11756 "version": "1.22.0", 11757 "sha256": "0xrxl0b8lmjhqsdvm1glirj5yvs3ml94cl2zrj36yp7rc1yn2aq1", 11758 "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "EDASeq", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RUVSeq", "Rsamtools", "Rsubread", "S4Vectors", "Seqinfo", "XVector", "cluster", "ggExtra", "ggfittext", "ggplot2", "ggrepel", "motifStack", "rtracklayer", "scales", "txdbmaker"] 11759 }, 11760 "rifi": { 11761 "name": "rifi", 11762 "version": "1.14.0", 11763 "sha256": "1gq05wxw0dd625m5y5y3cwr2gwmm3n3vkl75ghxcsas0yz5vs0s7", 11764 "depends": ["S4Vectors", "SummarizedExperiment", "car", "cowplot", "doMC", "dplyr", "egg", "foreach", "ggplot2", "nls2", "nnet", "reshape2", "rlang", "rtracklayer", "scales", "stringr", "tibble"] 11765 }, 11766 "rifiComparative": { 11767 "name": "rifiComparative", 11768 "version": "1.10.0", 11769 "sha256": "0ywwdh8ashi55wgw34qd0ba460pj2wvv8v0i388fk6fpqanzxcm0", 11770 "depends": ["DTA", "LSD", "S4Vectors", "SummarizedExperiment", "cowplot", "devtools", "doMC", "dplyr", "egg", "foreach", "ggplot2", "ggrepel", "nnet", "reshape2", "rlang", "rtracklayer", "scales", "stringr", "tibble", "writexl"] 11771 }, 11772 "rigvf": { 11773 "name": "rigvf", 11774 "version": "1.2.0", 11775 "sha256": "1jimnych28qrpwsd82wpx1c24f8acap6b084ph5ccizpgyl3xbzr", 11776 "depends": ["GenomicRanges", "IRanges", "Seqinfo", "cachem", "dplyr", "httr2", "jsonlite", "memoise", "rjsoncons", "rlang", "tidyr", "whisker"] 11777 }, 11778 "rmelting": { 11779 "name": "rmelting", 11780 "version": "1.26.0", 11781 "sha256": "0sbhcfrf4r7d6rvdwnzb0kvj10x93c9srzaavc0y2jkgrqcvg1lw", 11782 "depends": ["Rdpack", "rJava"] 11783 }, 11784 "rmspc": { 11785 "name": "rmspc", 11786 "version": "1.16.0", 11787 "sha256": "0jsf4s8grc2qx4jqg8kii5jlvni4m1fqgvmaxdvicgpd15wx1qnp", 11788 "depends": ["BiocManager", "GenomicRanges", "processx", "rtracklayer", "stringr"] 11789 }, 11790 "rnaEditr": { 11791 "name": "rnaEditr", 11792 "version": "1.20.0", 11793 "sha256": "1f09d09l0flnjx4d54qwilwl861w5wc8p7b1xa8g99gj5qgjc57y", 11794 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "bumphunter", "corrplot", "logistf", "plyr", "survival"] 11795 }, 11796 "rnaseqcomp": { 11797 "name": "rnaseqcomp", 11798 "version": "1.40.0", 11799 "sha256": "1lq8d4lj11fyfhcikr9xj0c0a7v0bzw2a0x3kn95fxc30qmlrz98", 11800 "depends": ["RColorBrewer"] 11801 }, 11802 "roar": { 11803 "name": "roar", 11804 "version": "1.46.0", 11805 "sha256": "1cain3g3q7s25b2pqvwadxw67x4bkdq7czgv7diy2s68xky2zlri", 11806 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "rtracklayer"] 11807 }, 11808 "roastgsa": { 11809 "name": "roastgsa", 11810 "version": "1.8.0", 11811 "sha256": "0c2ydbhvnaczlhh6zk1srfq6pswc67y82v5wcpbqpskxa4q1x0dv", 11812 "depends": ["Biobase", "RColorBrewer", "ggplot2", "gplots", "limma"] 11813 }, 11814 "ropls": { 11815 "name": "ropls", 11816 "version": "1.42.0", 11817 "sha256": "0wlldfra8cvagb1125lh3qmrf774d7jf9mfnqnd7mv9s2c6lms0d", 11818 "depends": ["Biobase", "MultiAssayExperiment", "MultiDataSet", "SummarizedExperiment", "ggplot2", "plotly"] 11819 }, 11820 "rprimer": { 11821 "name": "rprimer", 11822 "version": "1.14.0", 11823 "sha256": "02hj8qfjbv4p9gw52fyx8klxxg3iwa76agsqj8zzwz9d7pjgqk6b", 11824 "depends": ["Biostrings", "DT", "IRanges", "S4Vectors", "bslib", "ggplot2", "mathjaxr", "patchwork", "reshape2", "shiny", "shinyFeedback", "shinycssloaders"] 11825 }, 11826 "rpx": { 11827 "name": "rpx", 11828 "version": "2.18.0", 11829 "sha256": "15f25i5854hmlvw9kvf603pj83di80whlj5c3ij030wdq1g4813b", 11830 "depends": ["BiocFileCache", "RCurl", "curl", "jsonlite", "xml2"] 11831 }, 11832 "rqt": { 11833 "name": "rqt", 11834 "version": "1.36.0", 11835 "sha256": "1kwn9x0avaj04hlb3blps4qa94czcv3d9dh57xsklqp1jkcdmcmf", 11836 "depends": ["CompQuadForm", "Matrix", "RUnit", "SummarizedExperiment", "car", "glmnet", "metap", "pls", "ropls"] 11837 }, 11838 "rqubic": { 11839 "name": "rqubic", 11840 "version": "1.56.0", 11841 "sha256": "0ffp657yhaj4agd7lgrqcwqqnw6lcybmf1wzahd334vgwi3sz2xp", 11842 "depends": ["Biobase", "BiocGenerics", "biclust"] 11843 }, 11844 "rrvgo": { 11845 "name": "rrvgo", 11846 "version": "1.22.0", 11847 "sha256": "0nldapswvf69mdcizynz4cjv2wdf3f24qjl4xsq4cqhzmx5xgjl2", 11848 "depends": ["AnnotationDbi", "GOSemSim", "GO_db", "ggplot2", "ggrepel", "pheatmap", "shiny", "tm", "treemap", "umap", "wordcloud"] 11849 }, 11850 "rsbml": { 11851 "name": "rsbml", 11852 "version": "2.68.0", 11853 "sha256": "094h37sdg76365khhablm6wf8mpqbmr151xl83yfv6ld1zilqz9m", 11854 "depends": ["BiocGenerics", "graph"] 11855 }, 11856 "rsemmed": { 11857 "name": "rsemmed", 11858 "version": "1.20.0", 11859 "sha256": "1f06l7jlmpcf61dc9szx9h2ajvj6vfh57zkgnpfzl9dx33lyj2yw", 11860 "depends": ["dplyr", "igraph", "magrittr", "stringr"] 11861 }, 11862 "rtracklayer": { 11863 "name": "rtracklayer", 11864 "version": "1.70.0", 11865 "sha256": "1i9yx0ngx97lmw7pcdj89da6bb0w6gpc98mrwy9prlmml78d81dn", 11866 "depends": ["BiocGenerics", "BiocIO", "Biostrings", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "XML", "XVector", "curl", "httr", "restfulr"] 11867 }, 11868 "runibic": { 11869 "name": "runibic", 11870 "version": "1.32.0", 11871 "sha256": "0zvvkwwkrr7lrcf3rzx98gmb7sz36hn18mkiim0qbk1r576xpgdv", 11872 "depends": ["Rcpp", "SummarizedExperiment", "biclust", "testthat"] 11873 }, 11874 "sRACIPE": { 11875 "name": "sRACIPE", 11876 "version": "2.2.0", 11877 "sha256": "1hkb3k4snawgfj68d2cx5320dgl6grdpd5rvxcjf8gaxmyl3vj4k", 11878 "depends": ["BiocGenerics", "MASS", "RColorBrewer", "Rcpp", "S4Vectors", "SummarizedExperiment", "doFuture", "doRNG", "foreach", "future", "ggplot2", "gplots", "gridExtra", "htmlwidgets", "reshape2", "umap", "visNetwork"] 11879 }, 11880 "sSNAPPY": { 11881 "name": "sSNAPPY", 11882 "version": "1.14.0", 11883 "sha256": "0jlg8apky668mqgf2xzqxd0555xhfbj8lhdvjp12rc7pfq3ylnks", 11884 "depends": ["SummarizedExperiment", "dplyr", "edgeR", "ggforce", "ggplot2", "ggraph", "graphite", "gtools", "igraph", "magrittr", "org_Hs_eg_db", "pheatmap", "reshape2", "rlang", "stringr", "tibble", "tidyr"] 11885 }, 11886 "sSeq": { 11887 "name": "sSeq", 11888 "version": "1.48.0", 11889 "sha256": "1icbgrck6v8mwmmbbrc2qqgk15dmjzbp40nr03jc5v3rlh6m42r1", 11890 "depends": ["RColorBrewer", "caTools"] 11891 }, 11892 "safe": { 11893 "name": "safe", 11894 "version": "3.50.0", 11895 "sha256": "1p4lscs7dasag6qfv4s98adgz1sp6q08a3agf8z96qbzg1gvw0c9", 11896 "depends": ["AnnotationDbi", "Biobase", "SparseM"] 11897 }, 11898 "sagenhaft": { 11899 "name": "sagenhaft", 11900 "version": "1.80.0", 11901 "sha256": "16m68j9p9ad7x1mwbgpzivhn60y5z4h66kaqpgkzk7wn61lajxh4", 11902 "depends": ["SparseM"] 11903 }, 11904 "sangeranalyseR": { 11905 "name": "sangeranalyseR", 11906 "version": "1.19.0", 11907 "sha256": "0hji6y9ya7bg437rcsm2l0dibpzgyrh73kv5h7gdkxwmmx97fbaj", 11908 "depends": ["BiocStyle", "Biostrings", "DECIPHER", "DT", "ape", "data_table", "excelR", "ggdendro", "gridExtra", "knitr", "logger", "openxlsx", "plotly", "pwalign", "reshape2", "rmarkdown", "sangerseqR", "seqinr", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "shinyjs", "stringr", "zeallot"] 11909 }, 11910 "sangerseqR": { 11911 "name": "sangerseqR", 11912 "version": "1.46.0", 11913 "sha256": "1hjadhr64qk91byd5cswsjvqggjczjz8cprjiarmf389bfcf0786", 11914 "depends": ["Biostrings", "pwalign", "shiny", "stringr"] 11915 }, 11916 "sarks": { 11917 "name": "sarks", 11918 "version": "1.22.0", 11919 "sha256": "0bkkhi5cpbmwc6f1l1vv7mkz4z76mq1sqam3yq3hmjhhxihf8ffx", 11920 "depends": ["Biostrings", "IRanges", "binom", "cluster", "rJava"] 11921 }, 11922 "saseR": { 11923 "name": "saseR", 11924 "version": "1.6.0", 11925 "sha256": "0gms4md6qhw2fbbl2sn31fa50abpp19wmm6qh2z048v08zyf3wfb", 11926 "depends": ["ASpli", "BiocGenerics", "BiocParallel", "DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "MatrixGenerics", "PRROC", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "edgeR", "igraph", "limma"] 11927 }, 11928 "satuRn": { 11929 "name": "satuRn", 11930 "version": "1.18.0", 11931 "sha256": "0xfylzpbnqjm8d38l7w7cvqlncpca2cj607rg4vfpsslykmqii05", 11932 "depends": ["BiocParallel", "Matrix", "SummarizedExperiment", "boot", "ggplot2", "limma", "locfdr", "pbapply"] 11933 }, 11934 "scAnnotatR": { 11935 "name": "scAnnotatR", 11936 "version": "1.16.0", 11937 "sha256": "1r9c033066rdrcnh0d540ln8axsmzpqjb35gxasmrfbd5zgl2m6h", 11938 "depends": ["AnnotationHub", "ROCR", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "ape", "caret", "data_tree", "dplyr", "e1071", "ggplot2", "kernlab", "pROC"] 11939 }, 11940 "scBFA": { 11941 "name": "scBFA", 11942 "version": "1.24.0", 11943 "sha256": "0fdnh210afa30z9vjbdz58p47f14n4h6lm6jrvj8hi87wdxjk2lh", 11944 "depends": ["DESeq2", "MASS", "Matrix", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "copula", "ggplot2", "zinbwave"] 11945 }, 11946 "scBubbletree": { 11947 "name": "scBubbletree", 11948 "version": "1.12.0", 11949 "sha256": "1pcpja5x0ax1788csykzr08p0h1c1z6vrv4njvy4f2fdj971czwr", 11950 "depends": ["BiocParallel", "Seurat", "ape", "dplyr", "ggplot2", "ggtree", "patchwork", "proxy", "reshape2", "scales"] 11951 }, 11952 "scCB2": { 11953 "name": "scCB2", 11954 "version": "1.20.0", 11955 "sha256": "0laxia6dkd00iq0ri10v771y6rspa920q78b2ajxq79j4qadn5l9", 11956 "depends": ["DropletUtils", "Matrix", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "doParallel", "edgeR", "foreach", "iterators", "rhdf5"] 11957 }, 11958 "scClassify": { 11959 "name": "scClassify", 11960 "version": "1.22.0", 11961 "sha256": "1napk4jijjqan6x0y0xxf7lkj1d8h7djala7r5npdn5cj7wjykln", 11962 "depends": ["BiocParallel", "Cepo", "Matrix", "S4Vectors", "cluster", "diptest", "ggplot2", "ggraph", "hopach", "igraph", "limma", "mgcv", "minpack_lm", "mixtools", "proxy", "proxyC", "statmod"] 11963 }, 11964 "scDD": { 11965 "name": "scDD", 11966 "version": "1.34.0", 11967 "sha256": "03zxkw6jx7gd37vj1li4z54sfw94khv5h962inzx2iazsa774wbh", 11968 "depends": ["BiocParallel", "EBSeq", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "arm", "fields", "ggplot2", "mclust", "outliers", "scran"] 11969 }, 11970 "scDDboost": { 11971 "name": "scDDboost", 11972 "version": "1.12.0", 11973 "sha256": "0fzmk0wj7qs7jcdsqd12qmhk9gd23pagimgf1xbn0clasy800zp5", 11974 "depends": ["BH", "BiocParallel", "EBSeq", "Oscope", "Rcpp", "RcppEigen", "SingleCellExperiment", "SummarizedExperiment", "cluster", "ggplot2", "mclust"] 11975 }, 11976 "scDataviz": { 11977 "name": "scDataviz", 11978 "version": "1.20.0", 11979 "sha256": "1q7hac56lakzs10dr9kzq2m817m4891acgjccfixgcfsvdc72svl", 11980 "depends": ["MASS", "RColorBrewer", "S4Vectors", "Seurat", "SingleCellExperiment", "corrplot", "flowCore", "ggplot2", "ggrepel", "matrixStats", "reshape2", "scales", "umap"] 11981 }, 11982 "scDblFinder": { 11983 "name": "scDblFinder", 11984 "version": "1.24.0", 11985 "sha256": "0l9zhcx4a3wdzldlsg4blq3jh259pwd0h9qbhwwcz94jlp9v9wjq", 11986 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "Matrix", "Rsamtools", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bluster", "igraph", "rtracklayer", "scater", "scran", "scuttle", "xgboost"] 11987 }, 11988 "scDesign3": { 11989 "name": "scDesign3", 11990 "version": "1.8.0", 11991 "sha256": "0pjd68c25badgw9gz44zfcg6w5m9kbvqffjw2ppvi60y7vz0dal9", 11992 "depends": ["BiocParallel", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "coop", "dplyr", "gamlss", "gamlss_dist", "ggplot2", "irlba", "matrixStats", "mclust", "mgcv", "mvtnorm", "pbmcapply", "sparseMVN", "tibble", "umap", "viridis"] 11993 }, 11994 "scDiagnostics": { 11995 "name": "scDiagnostics", 11996 "version": "1.4.0", 11997 "sha256": "1fgpp6gkgwr0lkkbi88rhxb1jdzcjx5jz94k4jasnxm62wcb7r50", 11998 "depends": ["FNN", "GGally", "MASS", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "bluster", "cramer", "ggplot2", "ggridges", "igraph", "isotree", "ranger", "rlang", "scales", "stringr", "transport"] 11999 }, 12000 "scDotPlot": { 12001 "name": "scDotPlot", 12002 "version": "1.4.0", 12003 "sha256": "07c5sxf9nfk2976zrh1gyz2qhdb6lp65iilyvlw7jzsikyx1hh41", 12004 "depends": ["BiocGenerics", "Seurat", "SingleCellExperiment", "aplot", "cli", "dplyr", "ggplot2", "ggsci", "ggtree", "magrittr", "purrr", "rlang", "scales", "scater", "stringr", "tibble", "tidyr"] 12005 }, 12006 "scFeatureFilter": { 12007 "name": "scFeatureFilter", 12008 "version": "1.30.0", 12009 "sha256": "0p3aacnj32nnwn8s7ywngs63gf0cciw517a42b610fzn0nf93b4w", 12010 "depends": ["dplyr", "ggplot2", "magrittr", "rlang", "tibble"] 12011 }, 12012 "scGPS": { 12013 "name": "scGPS", 12014 "version": "1.24.0", 12015 "sha256": "0ck8sjxfmb5ls7192yp82bczwwhgf5kqaqivniikhdbb6gy0ilvy", 12016 "depends": ["DESeq2", "Rcpp", "RcppArmadillo", "RcppParallel", "SingleCellExperiment", "SummarizedExperiment", "caret", "dplyr", "dynamicTreeCut", "fastcluster", "ggplot2", "glmnet", "locfit"] 12017 }, 12018 "scGraphVerse": { 12019 "name": "scGraphVerse", 12020 "version": "1.0.0", 12021 "sha256": "02nzhprhvvqk903cj7ynskz5dwbjsknd05wn2z8pwnx4na4h33hs", 12022 "depends": ["BiocBaseUtils", "BiocParallel", "GENIE3", "MASS", "Matrix", "MultiAssayExperiment", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "distributions3", "doParallel", "doRNG", "dplyr", "glmnet", "graph", "httr", "igraph", "jsonlite", "mpath", "reticulate", "tidyr"] 12023 }, 12024 "scHOT": { 12025 "name": "scHOT", 12026 "version": "1.22.0", 12027 "sha256": "1191rflc7ilcqnmfsgkh532x7mh5hbkg513aiv1zm24gw630jxjb", 12028 "depends": ["BiocParallel", "IRanges", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ggforce", "ggplot2", "igraph", "reshape"] 12029 }, 12030 "scHiCcompare": { 12031 "name": "scHiCcompare", 12032 "version": "1.2.0", 12033 "sha256": "17lan37g10hm8r9xn48rw21hyhby42mjfvpj5jj64hh4cjr8n3ky", 12034 "depends": ["BiocParallel", "HiCcompare", "data_table", "dplyr", "ggplot2", "gtools", "lattice", "mclust", "mice", "miceadds", "ranger", "rlang", "rstatix", "tidyr"] 12035 }, 12036 "scLANE": { 12037 "name": "scLANE", 12038 "version": "1.0.0", 12039 "sha256": "0g41wzi4jh12l3m85jw3acb92f49gybykjfj7y6s98vpv4ap0vii", 12040 "depends": ["MASS", "Matrix", "Rcpp", "RcppEigen", "bigstatsr", "broom_mixed", "doSNOW", "dplyr", "foreach", "furrr", "future", "gamlss", "geeM", "ggplot2", "glm2", "glmmTMB", "magrittr", "mpath", "purrr", "scales", "tidyr", "tidyselect", "withr"] 12041 }, 12042 "scMET": { 12043 "name": "scMET", 12044 "version": "1.12.0", 12045 "sha256": "1r7p3arjqvbxz46hlkh0a5ah3bckg4imxxhqfr8bp8f1i5wv7h6v", 12046 "depends": ["BH", "BiocStyle", "MASS", "Matrix", "Rcpp", "RcppEigen", "RcppParallel", "S4Vectors", "SingleCellExperiment", "StanHeaders", "SummarizedExperiment", "VGAM", "assertthat", "coda", "cowplot", "data_table", "dplyr", "ggplot2", "logitnorm", "matrixStats", "rstan", "rstantools", "viridis"] 12047 }, 12048 "scMerge": { 12049 "name": "scMerge", 12050 "version": "1.26.0", 12051 "sha256": "1z9g33sajhbirbafkvzl1cc0cwb6dsy79bmy3dw30z5awyfyjj4m", 12052 "depends": ["BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "M3Drop", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "batchelor", "cluster", "cvTools", "distr", "igraph", "proxyC", "ruv", "scater", "scran"] 12053 }, 12054 "scMitoMut": { 12055 "name": "scMitoMut", 12056 "version": "1.6.0", 12057 "sha256": "02443jab6l3760090x3qvi9zhk2d7nmkv1faibp9fgpdqms01aha", 12058 "depends": ["RColorBrewer", "Rcpp", "RcppArmadillo", "data_table", "ggplot2", "magrittr", "pheatmap", "plyr", "readr", "rhdf5", "stringr"] 12059 }, 12060 "scMultiSim": { 12061 "name": "scMultiSim", 12062 "version": "1.6.0", 12063 "sha256": "010gdscjvh49cas4b6n5lnalsasy7864ccvfjvbgm4ywq3y0q5fv", 12064 "depends": ["BiocParallel", "KernelKnn", "MASS", "Rtsne", "SummarizedExperiment", "ape", "assertthat", "crayon", "dplyr", "foreach", "ggplot2", "gplots", "igraph", "markdown", "matrixStats", "phytools", "rlang", "zeallot"] 12065 }, 12066 "scPCA": { 12067 "name": "scPCA", 12068 "version": "1.24.0", 12069 "sha256": "0m0qc7i2pqag4r5i9ly35fp7vqnhlfb5jimnk0yfkx5bj0bd9ya8", 12070 "depends": ["BiocParallel", "DelayedArray", "Matrix", "MatrixGenerics", "RSpectra", "Rdpack", "ScaledMatrix", "assertthat", "cluster", "coop", "dplyr", "elasticnet", "kernlab", "matrixStats", "origami", "purrr", "sparsepca", "stringr", "tibble"] 12071 }, 12072 "scPipe": { 12073 "name": "scPipe", 12074 "version": "2.10.0", 12075 "sha256": "1y6fmydg0l67v8g830h52pwx9nd2bv5gd15skah1znrjam99vali", 12076 "depends": ["AnnotationDbi", "BiocGenerics", "Biostrings", "DropletUtils", "GGally", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "Matrix", "MultiAssayExperiment", "Rcpp", "Rhtslib", "Rsamtools", "Rsubread", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "basilisk", "biomaRt", "data_table", "dplyr", "flexmix", "ggplot2", "glue", "hash", "magrittr", "mclust", "org_Hs_eg_db", "org_Mm_eg_db", "purrr", "reshape", "reticulate", "rlang", "robustbase", "rtracklayer", "scales", "stringr", "testthat", "tibble", "tidyr", "vctrs"] 12077 }, 12078 "scRNAseqApp": { 12079 "name": "scRNAseqApp", 12080 "version": "1.10.0", 12081 "sha256": "1z300l667y9pn195rmc92a59v56zxmvjrsxbc073693wbwvwp1yi", 12082 "depends": ["ComplexHeatmap", "DBI", "DT", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "RColorBrewer", "RSQLite", "RefManageR", "Rsamtools", "S4Vectors", "Seurat", "SeuratObject", "SingleCellExperiment", "bibtex", "bslib", "circlize", "colourpicker", "data_table", "fs", "ggdendro", "ggforce", "ggplot2", "ggrepel", "ggridges", "gridExtra", "htmltools", "jsonlite", "magrittr", "patchwork", "plotly", "reshape2", "rhdf5", "rtracklayer", "scales", "scrypt", "shiny", "shinyhelper", "shinymanager", "slingshot", "sortable", "xfun", "xml2"] 12083 }, 12084 "scReClassify": { 12085 "name": "scReClassify", 12086 "version": "1.16.0", 12087 "sha256": "1bwbm2la5wcafisj6xprqg5y4yj0gxxhgmqkz9q6cd8ssfnr0bw6", 12088 "depends": ["SingleCellExperiment", "SummarizedExperiment", "e1071", "randomForest"] 12089 }, 12090 "scRecover": { 12091 "name": "scRecover", 12092 "version": "1.26.0", 12093 "sha256": "1nlzrrn4brf2615qj0ynxfpzddx7238nxhbsxp5c333slvncqy8x", 12094 "depends": ["BiocParallel", "MASS", "Matrix", "SAVER", "bbmle", "doParallel", "foreach", "gamlss", "kernlab", "penalized", "preseqR", "pscl", "rsvd"] 12095 }, 12096 "scRepertoire": { 12097 "name": "scRepertoire", 12098 "version": "2.5.8", 12099 "sha256": "0ijycpmaivcqqmdc90h5jx8rcwg9112pl2mdpms1hgvww70x3s6w", 12100 "depends": ["Matrix", "Rcpp", "S4Vectors", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "evmix", "ggalluvial", "ggdendro", "ggplot2", "ggraph", "iNEXT", "igraph", "immApex", "lifecycle", "purrr", "quantreg", "rjson", "rlang", "tidygraph"] 12101 }, 12102 "scShapes": { 12103 "name": "scShapes", 12104 "version": "1.16.0", 12105 "sha256": "1vs0ldcawicby8mbzpxz2szfjljf2pgb6rj231d3bbmn6975822g", 12106 "depends": ["BiocParallel", "MASS", "Matrix", "VGAM", "dgof", "emdbook", "magrittr", "pscl"] 12107 }, 12108 "scTGIF": { 12109 "name": "scTGIF", 12110 "version": "1.24.0", 12111 "sha256": "07fmcgvam3swbg254j9hhyj7x9sjvs9b0mrx60hxfd4rg1d0dsgf", 12112 "depends": ["Biobase", "BiocStyle", "GSEABase", "RColorBrewer", "Rcpp", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "igraph", "knitr", "msigdbr", "nnTensor", "plotly", "rmarkdown", "scales", "schex", "tagcloud", "tibble"] 12113 }, 12114 "scTHI": { 12115 "name": "scTHI", 12116 "version": "1.22.0", 12117 "sha256": "0jk38bqr1x17xkpwgxqpsdh9m4vvsccx1a00abqqs07rzfhacfs1", 12118 "depends": ["BiocParallel", "Rtsne"] 12119 }, 12120 "scTensor": { 12121 "name": "scTensor", 12122 "version": "2.20.0", 12123 "sha256": "0alipcy6hchw07rwxqib3w6vy5lycfxqrsbsazqmli1n2qblkjj3", 12124 "depends": ["AnnotationDbi", "AnnotationHub", "BiocManager", "BiocStyle", "Category", "DOSE", "GOstats", "MeSHDbi", "RSQLite", "ReactomePA", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "abind", "ccTensor", "checkmate", "crayon", "ggplot2", "heatmaply", "igraph", "knitr", "meshr", "nnTensor", "outliers", "plotly", "plotrix", "rTensor", "reactome_db", "rmarkdown", "schex", "tagcloud", "visNetwork"] 12125 }, 12126 "scTreeViz": { 12127 "name": "scTreeViz", 12128 "version": "1.16.0", 12129 "sha256": "0jm9ymw3vinzrsgn762yzrrvxxvbk4bgswa4hqfs6cacdhnsah0x", 12130 "depends": ["Matrix", "Rtsne", "S4Vectors", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "clustree", "data_table", "digest", "epivizr", "epivizrData", "epivizrServer", "ggplot2", "ggraph", "httr", "igraph", "scater", "scran", "sys"] 12131 }, 12132 "scafari": { 12133 "name": "scafari", 12134 "version": "1.0.0", 12135 "sha256": "0pwda9szl9ga8ic17wnfkadgisyzjy6gihvsrcn1ap6vdjzgs745", 12136 "depends": ["ComplexHeatmap", "DT", "GenomicRanges", "RANN", "R_utils", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "biomaRt", "circlize", "dbscan", "dplyr", "factoextra", "ggbio", "ggplot2", "httr", "igraph", "jsonlite", "magrittr", "markdown", "org_Hs_eg_db", "plotly", "reshape2", "rhdf5", "scales", "shiny", "shinyBS", "shinycssloaders", "shinycustomloader", "shinyjs", "stringr", "tibble", "tidyr", "txdbmaker", "waiter"] 12137 }, 12138 "scanMiR": { 12139 "name": "scanMiR", 12140 "version": "1.16.0", 12141 "sha256": "0yfzfsilqfm3waj4hjx455k7icln526jgmhp5byyq75zn3a8mgr8", 12142 "depends": ["BiocParallel", "Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "cowplot", "data_table", "ggplot2", "pwalign", "seqLogo", "stringi"] 12143 }, 12144 "scanMiRApp": { 12145 "name": "scanMiRApp", 12146 "version": "1.16.0", 12147 "sha256": "0mfmlvdlzn9ldxhfrx1szhkssqqwqzy7l943j2y2rfsavg3w14lj", 12148 "depends": ["AnnotationDbi", "AnnotationFilter", "AnnotationHub", "BiocParallel", "Biostrings", "DT", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "data_table", "digest", "ensembldb", "fst", "ggplot2", "htmlwidgets", "plotly", "rintrojs", "rtracklayer", "scanMiR", "scanMiRData", "shiny", "shinycssloaders", "shinydashboard", "shinyjqui", "txdbmaker", "waiter"] 12149 }, 12150 "scater": { 12151 "name": "scater", 12152 "version": "1.38.0", 12153 "sha256": "1qwygk8fg8nharrkmjs65fcl3lsdi232f2383s5j8vm1qil5gghd", 12154 "depends": ["BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "MatrixGenerics", "RColorBrewer", "RcppML", "Rtsne", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat", "ggbeeswarm", "ggplot2", "ggrastr", "ggrepel", "pheatmap", "rlang", "scuttle", "uwot", "viridis"] 12155 }, 12156 "scatterHatch": { 12157 "name": "scatterHatch", 12158 "version": "1.16.0", 12159 "sha256": "027gmj3ymx9f15rcymj30xggmf0rggs2jygw39mxf7iqak9r97kc", 12160 "depends": ["ggplot2", "plyr", "spatstat_geom"] 12161 }, 12162 "sccomp": { 12163 "name": "sccomp", 12164 "version": "2.2.0", 12165 "sha256": "06xnp6f962q6qc4078dcaqsh9cdvxgwlis4sinh90y96fmsph6qi", 12166 "depends": ["SingleCellExperiment", "boot", "cli", "crayon", "dplyr", "fansi", "forcats", "ggplot2", "ggrepel", "glue", "instantiate", "lifecycle", "magrittr", "patchwork", "purrr", "readr", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect"] 12167 }, 12168 "scde": { 12169 "name": "scde", 12170 "version": "2.38.0", 12171 "sha256": "1cmqzlqdb561jyd7yvga55wpx78bx8wlv3ilq5kwmawjd8x4yrf6", 12172 "depends": ["BiocParallel", "Cairo", "MASS", "RColorBrewer", "RMTstat", "Rcpp", "RcppArmadillo", "Rook", "edgeR", "extRemes", "flexmix", "mgcv", "nnet", "pcaMethods", "quantreg", "rjson"] 12173 }, 12174 "scds": { 12175 "name": "scds", 12176 "version": "1.26.0", 12177 "sha256": "1j0z0w8cw80mr9nll9lj6x8573cyi1hk0wlz5f1bm66c2pf4q547", 12178 "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "pROC", "xgboost"] 12179 }, 12180 "schex": { 12181 "name": "schex", 12182 "version": "1.24.0", 12183 "sha256": "0h3dh3vcdfvyx9rryjzagmgfxqspfz6khjwwficvc80izkbm5kj0", 12184 "depends": ["SingleCellExperiment", "cluster", "concaveman", "dplyr", "entropy", "ggforce", "ggplot2", "hexbin", "rlang"] 12185 }, 12186 "scider": { 12187 "name": "scider", 12188 "version": "1.8.0", 12189 "sha256": "1007qg5rm11mm6ljwn5jyfgiil1byfr69xy5hvvl10wfrvydryjy", 12190 "depends": ["BiocNeighbors", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SpatialPack", "SummarizedExperiment", "dbscan", "ggplot2", "hexDensity", "hexbin", "igraph", "irlba", "isoband", "janitor", "knitr", "lwgeom", "pheatmap", "plotly", "sf", "shiny", "spatstat_explore", "spatstat_geom", "uwot"] 12191 }, 12192 "scifer": { 12193 "name": "scifer", 12194 "version": "1.12.0", 12195 "sha256": "04sglgwsxnw8h4v03hv9vh7hrr97f83pmvyqy1axz5g37lhgrf49", 12196 "depends": ["Biostrings", "DECIPHER", "basilisk", "basilisk_utils", "data_table", "dplyr", "flowCore", "ggplot2", "gridExtra", "here", "kableExtra", "knitr", "plyr", "pwalign", "reticulate", "rlang", "rmarkdown", "sangerseqR", "scales", "stringr", "tibble"] 12197 }, 12198 "scmap": { 12199 "name": "scmap", 12200 "version": "1.32.0", 12201 "sha256": "1hjpf2ihjd48q0p1alrnmxkimxpd8l2k0ax2493141gcz39snv58", 12202 "depends": ["Biobase", "BiocGenerics", "Rcpp", "RcppArmadillo", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "e1071", "ggplot2", "googleVis", "matrixStats", "proxy", "randomForest", "reshape2"] 12203 }, 12204 "scmeth": { 12205 "name": "scmeth", 12206 "version": "1.30.0", 12207 "sha256": "0j977hw1rfm483rk793ihjw7ijxxvninx2h2i6g9im7v0n499f68", 12208 "depends": ["AnnotationHub", "BSgenome", "BiocGenerics", "Biostrings", "DT", "DelayedArray", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "Seqinfo", "SummarizedExperiment", "annotatr", "bsseq", "reshape2"] 12209 }, 12210 "scone": { 12211 "name": "scone", 12212 "version": "1.34.0", 12213 "sha256": "1mna7qf6mhjqq50gpr47kz3936qj3z7hv6jh3sx2yn6dsmi12agv", 12214 "depends": ["BiocParallel", "DelayedMatrixStats", "MatrixGenerics", "RColorBrewer", "RUVSeq", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "aroma_light", "boot", "class", "cluster", "compositions", "diptest", "edgeR", "fpc", "gplots", "hexbin", "limma", "matrixStats", "mixtools", "rARPACK", "rhdf5", "sparseMatrixStats"] 12215 }, 12216 "scoreInvHap": { 12217 "name": "scoreInvHap", 12218 "version": "1.32.0", 12219 "sha256": "0md5crlf4b62nmphxipai7jnpaz7mn2b8r08xjk31zx7skba266j", 12220 "depends": ["BiocParallel", "Biostrings", "GenomicRanges", "SummarizedExperiment", "VariantAnnotation", "snpStats"] 12221 }, 12222 "scoup": { 12223 "name": "scoup", 12224 "version": "1.4.0", 12225 "sha256": "03gaggdqxkxxx11lfrv21ransdlkmhwzbrn900sjqwn551maacj5", 12226 "depends": ["Biostrings", "Matrix"] 12227 }, 12228 "scp": { 12229 "name": "scp", 12230 "version": "1.20.0", 12231 "sha256": "0ah2zy4mi5h1ihrv02s6z5q814rbyx37zcgj11iy5ss5j9zqhli4", 12232 "depends": ["IHW", "MsCoreUtils", "MultiAssayExperiment", "QFeatures", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "ggrepel", "matrixStats", "metapod", "nipals"] 12233 }, 12234 "scran": { 12235 "name": "scran", 12236 "version": "1.38.0", 12237 "sha256": "1ac4fxj5adqrsgpcpqhk9sxlagaaq2w577xq751kqvxs54hj63n4", 12238 "depends": ["BH", "BiocGenerics", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "MatrixGenerics", "Rcpp", "S4Arrays", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "beachmat", "bluster", "dqrng", "edgeR", "igraph", "limma", "metapod", "scuttle", "statmod"] 12239 }, 12240 "scrapper": { 12241 "name": "scrapper", 12242 "version": "1.4.0", 12243 "sha256": "16lvbwby98zinykh6ybxwiswyv7072pmk9lv8sbi7mfqlh0agzfz", 12244 "depends": ["BiocNeighbors", "DelayedArray", "Rcpp", "Rigraphlib", "assorthead", "beachmat"] 12245 }, 12246 "screenCounter": { 12247 "name": "screenCounter", 12248 "version": "1.10.0", 12249 "sha256": "11d17blwgrifq5acj93sd5zy1ri0ygrzja8cw82dwnihrb30zmrq", 12250 "depends": ["BiocParallel", "Rcpp", "S4Vectors", "SummarizedExperiment"] 12251 }, 12252 "scruff": { 12253 "name": "scruff", 12254 "version": "1.28.0", 12255 "sha256": "0qm43s8jk601xl6rqqqsgycilnpk9a45rlwm7qg9fc0729jrwp81", 12256 "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Rsamtools", "Rsubread", "S4Vectors", "ShortRead", "SingleCellExperiment", "SummarizedExperiment", "data_table", "ggbio", "ggplot2", "ggthemes", "parallelly", "patchwork", "plyr", "rtracklayer", "scales", "stringdist", "txdbmaker"] 12257 }, 12258 "scry": { 12259 "name": "scry", 12260 "version": "1.22.0", 12261 "sha256": "1sffz2g1wqh8g2k21j10l87lbdff134sfcvg7b9xnaqicakly51l", 12262 "depends": ["BiocSingular", "DelayedArray", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "glmpca"] 12263 }, 12264 "scuttle": { 12265 "name": "scuttle", 12266 "version": "1.20.0", 12267 "sha256": "1m235brp8blyzx1z0j3acqgmssjhp2jnpb72i3a3c1f7nd225qaj", 12268 "depends": ["BiocGenerics", "BiocParallel", "DelayedArray", "GenomicRanges", "Matrix", "MatrixGenerics", "Rcpp", "S4Arrays", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "beachmat"] 12269 }, 12270 "scviR": { 12271 "name": "scviR", 12272 "version": "1.10.0", 12273 "sha256": "047y1drrpn6g5s8li34kcspgmy9pv7l2bclfxhxrrm0f5d6w6avh", 12274 "depends": ["BiocFileCache", "MatrixGenerics", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "basilisk", "limma", "pheatmap", "reticulate", "scater", "shiny"] 12275 }, 12276 "seahtrue": { 12277 "name": "seahtrue", 12278 "version": "1.4.0", 12279 "sha256": "16j5l6gw8m7cwh5hwfmg4cr7qrw4wchpp93pckjgx2wznchkylz6", 12280 "depends": ["RColorBrewer", "cli", "colorspace", "dplyr", "forcats", "ggplot2", "ggridges", "glue", "janitor", "logger", "lubridate", "purrr", "readr", "readxl", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyxl", "validate"] 12281 }, 12282 "sechm": { 12283 "name": "sechm", 12284 "version": "1.18.0", 12285 "sha256": "0zjmz0s7z5wpfzf2w3rrfh8gq03m3l42kzha7h6x8wv7qx2clzf0", 12286 "depends": ["ComplexHeatmap", "S4Vectors", "SummarizedExperiment", "circlize", "matrixStats", "randomcoloR", "seriation"] 12287 }, 12288 "segmentSeq": { 12289 "name": "segmentSeq", 12290 "version": "2.44.0", 12291 "sha256": "06wwpk0l3zy2xajagxdhccnynpb8wqsj3ksdf4vm010a41rlqiwm", 12292 "depends": ["GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "ShortRead", "abind", "baySeq"] 12293 }, 12294 "segmenter": { 12295 "name": "segmenter", 12296 "version": "1.16.0", 12297 "sha256": "12ss0b59xcv6mhrfiway6k7cvgsgxlh71jjv8mvlv66gd5jxlxvj", 12298 "depends": ["ChIPseeker", "ComplexHeatmap", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "bamsignals", "chromhmmData"] 12299 }, 12300 "selectKSigs": { 12301 "name": "selectKSigs", 12302 "version": "1.22.0", 12303 "sha256": "12w82vm9ha1rbirwc361w2x719bskn53mrfaarm6ndcr37xz6lzl", 12304 "depends": ["HiLDA", "Rcpp", "gtools", "magrittr"] 12305 }, 12306 "semisup": { 12307 "name": "semisup", 12308 "version": "1.34.0", 12309 "sha256": "1ppy36h6qrrya4rwa7mz2bmrn1izj1397mrpx151y4vmniijf9v7", 12310 "depends": ["VGAM"] 12311 }, 12312 "seq_hotSPOT": { 12313 "name": "seq.hotSPOT", 12314 "version": "1.10.0", 12315 "sha256": "18a71gzl76wdmzckpvzg131nyxzkwzsdhny5n24ngjwgp6gg9q4k", 12316 "depends": ["R_utils", "hash"] 12317 }, 12318 "seqCAT": { 12319 "name": "seqCAT", 12320 "version": "1.32.0", 12321 "sha256": "1di2xcrsqjwcxzw6w93a777vfahnwcqxrfgnav3vagc11bdc99ri", 12322 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "dplyr", "ggplot2", "rlang", "rtracklayer", "scales", "tidyr"] 12323 }, 12324 "seqLogo": { 12325 "name": "seqLogo", 12326 "version": "1.76.0", 12327 "sha256": "189zhnm7rx0lya1xsn89as2c6awkidv641rri7w39ds0kygcy8x4", 12328 "depends": [] 12329 }, 12330 "seqPattern": { 12331 "name": "seqPattern", 12332 "version": "1.42.0", 12333 "sha256": "107l52mv68bpmjrhfgjm94wqxc3bqz1vhr2hd8rn6jzlwbn6bijj", 12334 "depends": ["Biostrings", "GenomicRanges", "IRanges", "KernSmooth", "plotrix"] 12335 }, 12336 "seqcombo": { 12337 "name": "seqcombo", 12338 "version": "1.32.0", 12339 "sha256": "12xf0cyrmbp4ybvc48yw96ggh5f8354ag065qm76g324zfd3c9iy", 12340 "depends": ["ggplot2", "igraph", "yulab_utils"] 12341 }, 12342 "seqsetvis": { 12343 "name": "seqsetvis", 12344 "version": "1.30.0", 12345 "sha256": "080njbczm82xy65z3lz1v5fxcvb5l4qamfjnxw73ib3by3wdskzr", 12346 "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "S4Vectors", "Seqinfo", "UpSetR", "cowplot", "data_table", "eulerr", "ggplot2", "ggplotify", "limma", "pbapply", "pbmcapply", "png", "rtracklayer", "scales"] 12347 }, 12348 "sesame": { 12349 "name": "sesame", 12350 "version": "1.28.0", 12351 "sha256": "0268p9yvzsnrjjbmbyqzhz9vnc6227200639kyn7yi2daa6fkzav", 12352 "depends": ["BiocFileCache", "BiocParallel", "GenomicRanges", "IRanges", "MASS", "S4Vectors", "Seqinfo", "SummarizedExperiment", "dplyr", "ggplot2", "preprocessCore", "readr", "reshape2", "sesameData", "stringr", "tibble", "wheatmap"] 12353 }, 12354 "sevenC": { 12355 "name": "sevenC", 12356 "version": "1.30.0", 12357 "sha256": "1sxydda3czgj2schk2wlpyxcms4p999ywxj1k3rvqb0jssxl8cfi", 12358 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "InteractionSet", "S4Vectors", "Seqinfo", "boot", "data_table", "purrr", "readr", "rtracklayer"] 12359 }, 12360 "sevenbridges": { 12361 "name": "sevenbridges", 12362 "version": "1.40.0", 12363 "sha256": "1kayxyhx3j9ni7cy8lynrnk8s05nckc8cj5x3nzhzqg6i58dddcx", 12364 "depends": ["S4Vectors", "curl", "data_table", "docopt", "httr", "jsonlite", "objectProperties", "stringr", "uuid", "yaml"] 12365 }, 12366 "shinyDSP": { 12367 "name": "shinyDSP", 12368 "version": "1.2.0", 12369 "sha256": "01d2y1knx34zc7afrd18s4macxb3x4vksfrwnd4md9dmfrdayxn3", 12370 "depends": ["AnnotationHub", "BiocGenerics", "ComplexHeatmap", "DT", "ExperimentHub", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bsicons", "bslib", "circlize", "cowplot", "dplyr", "edgeR", "ggplot2", "ggpubr", "ggrepel", "htmltools", "limma", "magrittr", "pals", "readr", "scales", "scater", "shiny", "shinyWidgets", "shinycssloaders", "shinyjs", "shinyvalidate", "standR", "stringr", "tibble", "tidyr", "withr"] 12371 }, 12372 "shinyMethyl": { 12373 "name": "shinyMethyl", 12374 "version": "1.46.0", 12375 "sha256": "1p3hphp5b3r8wax2hhlkb1ifzqhqwl7yxnsjn4c2mhsi4im2ych0", 12376 "depends": ["Biobase", "BiocGenerics", "MatrixGenerics", "RColorBrewer", "htmltools", "minfi", "shiny"] 12377 }, 12378 "shinybiocloader": { 12379 "name": "shinybiocloader", 12380 "version": "1.0.0", 12381 "sha256": "0hzkqbibmv8zsychb09babp4x895smvwfs8dpn75ic3ri7fx806k", 12382 "depends": ["htmltools", "shiny"] 12383 }, 12384 "shinyepico": { 12385 "name": "shinyepico", 12386 "version": "1.18.0", 12387 "sha256": "0d4v6jir613fmqvmcz9s3y9fpdamj0h8mbdnqkxf60z2k1881vdr", 12388 "depends": ["DT", "GenomicRanges", "data_table", "doParallel", "dplyr", "foreach", "ggplot2", "gplots", "heatmaply", "limma", "minfi", "plotly", "reshape2", "rlang", "rmarkdown", "rtracklayer", "shiny", "shinyWidgets", "shinycssloaders", "shinyjs", "shinythemes", "statmod", "tidyr", "zip"] 12389 }, 12390 "sigFeature": { 12391 "name": "sigFeature", 12392 "version": "1.28.0", 12393 "sha256": "0m0mqrg5hy0r6iaj7swnhb5s8x6j99rpagc38kynh4vahb6picq9", 12394 "depends": ["BiocParallel", "Matrix", "RColorBrewer", "SparseM", "SummarizedExperiment", "biocViews", "e1071", "nlme", "openxlsx", "pheatmap"] 12395 }, 12396 "siggenes": { 12397 "name": "siggenes", 12398 "version": "1.84.0", 12399 "sha256": "1rz5yi9lb5qkw6ix0sv6yj3533wxvvwwpb0955lzfm5w06r46sff", 12400 "depends": ["Biobase", "multtest", "scrime"] 12401 }, 12402 "sights": { 12403 "name": "sights", 12404 "version": "1.36.0", 12405 "sha256": "0awmi684h1gdv9a1yyz06yrdw6c81af54fw79bddwmf5yxfaxkcs", 12406 "depends": ["MASS", "ggplot2", "lattice", "qvalue", "reshape2"] 12407 }, 12408 "signatureSearch": { 12409 "name": "signatureSearch", 12410 "version": "1.24.0", 12411 "sha256": "1c8jykqfsbpmpn52svaqkg2da2gzdyyfd96hm1sfwx15z02sg9cw", 12412 "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "DOSE", "DelayedArray", "ExperimentHub", "GSEABase", "HDF5Array", "Matrix", "RSQLite", "Rcpp", "SummarizedExperiment", "clusterProfiler", "data_table", "dplyr", "fastmatch", "fgsea", "ggplot2", "magrittr", "org_Hs_eg_db", "qvalue", "reactome_db", "readr", "reshape2", "rhdf5", "scales", "tibble", "visNetwork"] 12413 }, 12414 "signeR": { 12415 "name": "signeR", 12416 "version": "2.12.0", 12417 "sha256": "1nlhxsq6v6nyadmfkyvibvgc9zg0r0s6lr5h60kvc1337ar8qzd4", 12418 "depends": ["BSgenome", "BiocFileCache", "BiocGenerics", "Biostrings", "DT", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS", "NMF", "PMCMRplus", "RColorBrewer", "Rcpp", "RcppArmadillo", "VGAM", "VariantAnnotation", "ada", "broom", "bsplus", "class", "clue", "cowplot", "dplyr", "e1071", "future", "future_apply", "ggplot2", "ggpubr", "glmnet", "kknn", "listenv", "magrittr", "maxstat", "nloptr", "pROC", "pheatmap", "ppclust", "proxy", "pvclust", "randomForest", "readr", "reshape2", "rtracklayer", "scales", "shiny", "shinyWidgets", "shinycssloaders", "shinydashboard", "survival", "survminer", "tibble", "tidyr"] 12419 }, 12420 "signifinder": { 12421 "name": "signifinder", 12422 "version": "1.12.0", 12423 "sha256": "0apncbw90r1svawz7g76w13ai7djf04709mmr0anb27m1i74aa34", 12424 "depends": ["AnnotationDbi", "BiocGenerics", "ComplexHeatmap", "DGEobj_utils", "GSVA", "IRanges", "RColorBrewer", "SpatialExperiment", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "consensusOV", "cowplot", "dplyr", "ensembldb", "ggplot2", "ggridges", "magrittr", "matrixStats", "maxstat", "openair", "org_Hs_eg_db", "patchwork", "scales", "survival", "survminer", "viridis"] 12425 }, 12426 "sigsquared": { 12427 "name": "sigsquared", 12428 "version": "1.42.0", 12429 "sha256": "1qm25yx8ykf35alqz8z0ky7akhc2zyzm568kfms6ravd0p41nyrk", 12430 "depends": ["Biobase", "survival"] 12431 }, 12432 "simPIC": { 12433 "name": "simPIC", 12434 "version": "1.6.0", 12435 "sha256": "1qr70cz04grmawsz3ir5ycaj74782c66mf2ing5zlndh3z3vv696", 12436 "depends": ["BiocGenerics", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "actuar", "checkmate", "edgeR", "fitdistrplus", "matrixStats", "rlang", "scales", "scuttle", "withr"] 12437 }, 12438 "similaRpeak": { 12439 "name": "similaRpeak", 12440 "version": "1.42.0", 12441 "sha256": "0s6602qzk8m9rnmifg17hpxj9f9i77lasg77ls7595n8ykb1l2kc", 12442 "depends": ["R6"] 12443 }, 12444 "simona": { 12445 "name": "simona", 12446 "version": "1.8.0", 12447 "sha256": "0fv5qqlchbij486w2j7r2yndj2c497f4id0skq3r8pp735lgc84j", 12448 "depends": ["ComplexHeatmap", "GetoptLong", "GlobalOptions", "Polychrome", "Rcpp", "S4Vectors", "circlize", "fastmatch", "igraph", "matrixStats", "shiny", "xml2"] 12449 }, 12450 "simpleSeg": { 12451 "name": "simpleSeg", 12452 "version": "1.12.0", 12453 "sha256": "1g0x3qc5ys0clwqw7vny7ld42n894xwpabxxnkyln610z30ifb6q", 12454 "depends": ["BiocParallel", "EBImage", "S4Vectors", "SummarizedExperiment", "cytomapper", "spatstat_geom", "terra"] 12455 }, 12456 "simplifyEnrichment": { 12457 "name": "simplifyEnrichment", 12458 "version": "2.4.0", 12459 "sha256": "1vz0pjn8j3ia6gcwdlr1c8cxvdbhf6rscag1r7h43gj3fxmsi9m0", 12460 "depends": ["AnnotationDbi", "ComplexHeatmap", "GO_db", "GetoptLong", "GlobalOptions", "circlize", "clue", "cluster", "colorspace", "digest", "simona", "slam", "tm"] 12461 }, 12462 "sincell": { 12463 "name": "sincell", 12464 "version": "1.42.0", 12465 "sha256": "1bnlw74nsi4as0x7azcjz52p9f3dw9zlhmc6iz37lvjkw75yany9", 12466 "depends": ["MASS", "Rcpp", "Rtsne", "TSP", "cluster", "entropy", "fastICA", "fields", "ggplot2", "igraph", "proxy", "reshape2", "scatterplot3d", "statmod"] 12467 }, 12468 "singleCellTK": { 12469 "name": "singleCellTK", 12470 "version": "2.20.0", 12471 "sha256": "17my62dn584mvzzsnzv1m4h95lj22bsp280pypxab6f2g7achs5a", 12472 "depends": ["AnnotationHub", "Biobase", "BiocParallel", "ComplexHeatmap", "DESeq2", "DT", "DelayedArray", "DelayedMatrixStats", "DropletUtils", "ExperimentHub", "GSEABase", "GSVA", "GSVAdata", "KernSmooth", "MAST", "Matrix", "ROCR", "R_utils", "Rtsne", "S4Vectors", "Seurat", "SingleCellExperiment", "SingleR", "SoupX", "SummarizedExperiment", "TENxPBMCData", "TSCAN", "TrajectoryUtils", "VAM", "anndata", "ape", "batchelor", "celda", "celldex", "circlize", "cluster", "colorspace", "colourpicker", "cowplot", "data_table", "dplyr", "eds", "enrichR", "ensembldb", "fields", "ggplot2", "ggplotify", "ggrepel", "ggtree", "gridExtra", "igraph", "lifecycle", "limma", "magrittr", "matrixStats", "metap", "msigdbr", "multtest", "plotly", "plyr", "reshape2", "reticulate", "rlang", "rmarkdown", "scDblFinder", "scMerge", "scRNAseq", "scater", "scds", "scran", "scuttle", "shiny", "shinyalert", "shinycssloaders", "shinyjs", "stringr", "sva", "tibble", "tidyr", "tximport", "withr", "yaml", "zellkonverter", "zinbwave"] 12473 }, 12474 "singscore": { 12475 "name": "singscore", 12476 "version": "1.30.0", 12477 "sha256": "1cyfhwwwq77ww5zdav17qzwh171h40dzi2plrzxqly808c5xxlqx", 12478 "depends": ["Biobase", "BiocParallel", "GSEABase", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "edgeR", "ggplot2", "ggrepel", "magrittr", "matrixStats", "plotly", "plyr", "reshape", "reshape2", "tidyr"] 12479 }, 12480 "sitadela": { 12481 "name": "sitadela", 12482 "version": "1.18.0", 12483 "sha256": "118hxyj6m2j5c3vz8c00nf2lh7hyz39vvmm0zpnsmnp84g5dlwmz", 12484 "depends": ["Biobase", "BiocGenerics", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "Rsamtools", "S4Vectors", "Seqinfo", "biomaRt", "rtracklayer", "txdbmaker"] 12485 }, 12486 "sitePath": { 12487 "name": "sitePath", 12488 "version": "1.26.0", 12489 "sha256": "1bldgb3jxx5jbk9fl0mc7hhdxscs73rbclchjj6695jl9rf267g4", 12490 "depends": ["RColorBrewer", "Rcpp", "ape", "aplot", "ggplot2", "ggrepel", "ggtree", "gridExtra", "seqinr", "tidytree"] 12491 }, 12492 "sizepower": { 12493 "name": "sizepower", 12494 "version": "1.80.0", 12495 "sha256": "054qgchvy9arxvdl3bwqiasn9x9p5cf9q79h5y95m06v82yp0iva", 12496 "depends": [] 12497 }, 12498 "sketchR": { 12499 "name": "sketchR", 12500 "version": "1.6.0", 12501 "sha256": "1hpnpspq9hiyx9yphcbz0z7ziq5fcj3nbci5zp3dnpiszpm7ahan", 12502 "depends": ["Biobase", "DelayedArray", "basilisk", "dplyr", "ggplot2", "reticulate", "rlang", "scales"] 12503 }, 12504 "skewr": { 12505 "name": "skewr", 12506 "version": "1.42.0", 12507 "sha256": "1fp9r69nnr6zn2awbqx9gyrlyg1i4v91yg1087pd49i33zs9nsdv", 12508 "depends": ["IlluminaHumanMethylation450kmanifest", "RColorBrewer", "S4Vectors", "methylumi", "minfi", "mixsmsn", "wateRmelon"] 12509 }, 12510 "slalom": { 12511 "name": "slalom", 12512 "version": "1.32.0", 12513 "sha256": "04l0pw0nm1s6j5s8jh577nzhsm38y7a4rvalplzcy8g9ppj64p5l", 12514 "depends": ["BH", "GSEABase", "Rcpp", "RcppArmadillo", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "rsvd"] 12515 }, 12516 "slingshot": { 12517 "name": "slingshot", 12518 "version": "2.18.0", 12519 "sha256": "1gsz2a3hsc5yc4kyxkqfb6dbyfmdp41bmnas714pvabnwrcapjwd", 12520 "depends": ["S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TrajectoryUtils", "igraph", "matrixStats", "princurve"] 12521 }, 12522 "smartid": { 12523 "name": "smartid", 12524 "version": "1.6.0", 12525 "sha256": "0iqnk5hpin79l43gzr6s29y7y79cd0w88lggrxsb2612nygpadd5", 12526 "depends": ["Matrix", "SummarizedExperiment", "dplyr", "ggplot2", "mclust", "mixtools", "sparseMatrixStats", "tidyr"] 12527 }, 12528 "smoothclust": { 12529 "name": "smoothclust", 12530 "version": "1.6.0", 12531 "sha256": "1mrz1z0ah33jksrhiyww9xwlk50sgb57hlqhbffi455lkjs4vj2i", 12532 "depends": ["BiocNeighbors", "Matrix", "SpatialExperiment", "SummarizedExperiment"] 12533 }, 12534 "smoppix": { 12535 "name": "smoppix", 12536 "version": "1.2.0", 12537 "sha256": "0xpv3x32jzfl9z82v6cayfm0fha64c27pv8r6sd9jzpffblkimxv", 12538 "depends": ["BiocParallel", "Rcpp", "Rdpack", "Rfast", "SpatialExperiment", "SummarizedExperiment", "extraDistr", "ggplot2", "lme4", "lmerTest", "openxlsx", "scam", "spatstat_geom", "spatstat_model", "spatstat_random"] 12539 }, 12540 "snapcount": { 12541 "name": "snapcount", 12542 "version": "1.22.0", 12543 "sha256": "1v47chrbwghyxjmwp5jbzgjkgvrbj3ccy3kzwrqx1cv1sf0n5xgj", 12544 "depends": ["GenomicRanges", "IRanges", "Matrix", "R6", "SummarizedExperiment", "assertthat", "data_table", "httr", "jsonlite", "magrittr", "purrr", "rlang", "stringr"] 12545 }, 12546 "snifter": { 12547 "name": "snifter", 12548 "version": "1.20.0", 12549 "sha256": "04ln62j4pa8fb3b46vbnrx729j05agak7n6zgalbdbwwyjs6r6sn", 12550 "depends": ["assertthat", "basilisk", "irlba", "reticulate"] 12551 }, 12552 "snm": { 12553 "name": "snm", 12554 "version": "1.58.0", 12555 "sha256": "06lx70dw0iyqkvq1ps5hign6nldc88krxgx66xkvr7sk7v7fy3n9", 12556 "depends": ["corpcor", "lme4"] 12557 }, 12558 "snpStats": { 12559 "name": "snpStats", 12560 "version": "1.60.0", 12561 "sha256": "0fyh1qzhfkiqdksxcwpr76mmlk13c6mi0m27kcdr5frb77kv1sq9", 12562 "depends": ["BiocGenerics", "Matrix", "survival"] 12563 }, 12564 "sosta": { 12565 "name": "sosta", 12566 "version": "1.2.0", 12567 "sha256": "12hf6hyvip9ll2ipzhc9xs2s3y97gzwr55n6f23hhysd0n4qn9ds", 12568 "depends": ["EBImage", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "patchwork", "rlang", "sf", "smoothr", "spatstat_explore", "spatstat_geom", "spatstat_random", "terra"] 12569 }, 12570 "spARI": { 12571 "name": "spARI", 12572 "version": "1.0.0", 12573 "sha256": "10vspwy7882wlmlsm873sz8rah4zlm5mzwzz6y2cihry342hyqkp", 12574 "depends": ["BiocParallel", "Matrix", "Rcpp", "SpatialExperiment", "SummarizedExperiment"] 12575 }, 12576 "spaSim": { 12577 "name": "spaSim", 12578 "version": "1.12.0", 12579 "sha256": "1a5fb8d0yplg3chs9k4zrk12cdpzras37xnwv8372vzh75g2r1bc", 12580 "depends": ["RANN", "SpatialExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "spatstat_geom", "spatstat_random"] 12581 }, 12582 "spacexr": { 12583 "name": "spacexr", 12584 "version": "1.2.0", 12585 "sha256": "1bgvm4gxb10k4p3q9d299xry803zskxmaxcxdkqy25kw5wc9rvsq", 12586 "depends": ["BiocFileCache", "BiocParallel", "Matrix", "SpatialExperiment", "SummarizedExperiment", "ggplot2", "httr", "memoise", "quadprog", "scatterpie"] 12587 }, 12588 "sparrow": { 12589 "name": "sparrow", 12590 "version": "1.16.0", 12591 "sha256": "0zv0sccv0rm6jdyvzy4dgi3gir0zxb7r2pdl4g7qfms62ipim3bm", 12592 "depends": ["BiocGenerics", "BiocParallel", "BiocSet", "ComplexHeatmap", "DelayedMatrixStats", "GSEABase", "Matrix", "babelgene", "checkmate", "circlize", "data_table", "edgeR", "ggplot2", "irlba", "limma", "plotly", "viridis"] 12593 }, 12594 "sparseMatrixStats": { 12595 "name": "sparseMatrixStats", 12596 "version": "1.22.0", 12597 "sha256": "15kychrmj4r4mmyjygwi69ayfm3fwfyjfbp475xylnwixyr5v7s4", 12598 "depends": ["Matrix", "MatrixGenerics", "Rcpp", "matrixStats"] 12599 }, 12600 "sparsenetgls": { 12601 "name": "sparsenetgls", 12602 "version": "1.28.0", 12603 "sha256": "1bx8ypv17paz5kvbqmk2vd5cy1iciqmhprlrkhvl7v0shw61kcgc", 12604 "depends": ["MASS", "Matrix", "glmnet", "huge"] 12605 }, 12606 "spatialDE": { 12607 "name": "spatialDE", 12608 "version": "1.16.0", 12609 "sha256": "1v9kp5qd99zm5zmf18xinki9jjc5xk3b741x2fz3vbc5dv3gxzaz", 12610 "depends": ["Matrix", "SpatialExperiment", "SummarizedExperiment", "basilisk", "checkmate", "ggplot2", "ggrepel", "gridExtra", "reticulate", "scales"] 12611 }, 12612 "spatialFDA": { 12613 "name": "spatialFDA", 12614 "version": "1.2.0", 12615 "sha256": "1ddz26xncw3wmdy0jjxkaymrxgwd3i3rdcygq867zijrqqz7m0w1", 12616 "depends": ["ExperimentHub", "S4Vectors", "SpatialExperiment", "SummarizedExperiment", "dplyr", "fda", "ggplot2", "patchwork", "purrr", "refund", "scales", "spatstat_explore", "spatstat_geom", "tidyr"] 12617 }, 12618 "spatialSimGP": { 12619 "name": "spatialSimGP", 12620 "version": "1.4.0", 12621 "sha256": "1xixl5ih67lkr254mdmc22qp5x6q6qm4krdpcxxjbljzfqw4yksd", 12622 "depends": ["MASS", "SpatialExperiment", "SummarizedExperiment"] 12623 }, 12624 "specL": { 12625 "name": "specL", 12626 "version": "1.44.0", 12627 "sha256": "1bdsardyjf0gywjfgcrk2m3fmak5bd9brysn9cz7i7d9720xqs3y", 12628 "depends": ["DBI", "RSQLite", "protViz", "seqinr"] 12629 }, 12630 "speckle": { 12631 "name": "speckle", 12632 "version": "1.10.0", 12633 "sha256": "0wn4myrbxamy7qqwzvfq8lb24ayxs1y6hh865v4rrjqdx6flww74", 12634 "depends": ["Seurat", "SingleCellExperiment", "edgeR", "ggplot2", "limma"] 12635 }, 12636 "spicyR": { 12637 "name": "spicyR", 12638 "version": "1.22.0", 12639 "sha256": "00ljikrz4w3drqsfm8krm72nc1sg8wm0h18kfrifvfa6b9baydv0", 12640 "depends": ["BiocParallel", "ClassifyR", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cli", "concaveman", "coxme", "data_table", "dplyr", "ggforce", "ggh4x", "ggnewscale", "ggplot2", "ggthemes", "lifecycle", "lmerTest", "magrittr", "pheatmap", "rlang", "scales", "scam", "simpleSeg", "spatstat_explore", "spatstat_geom", "survival", "tibble", "tidyr"] 12641 }, 12642 "spikeLI": { 12643 "name": "spikeLI", 12644 "version": "2.70.0", 12645 "sha256": "09jbaxyx98haazh8hag0l2s8dzmn9djixvk4dvfs3ld9p80wknhg", 12646 "depends": [] 12647 }, 12648 "spiky": { 12649 "name": "spiky", 12650 "version": "1.16.0", 12651 "sha256": "02n2k80n6pwgdzllhf7kf38hb99hb43p2hbzw5k479brhjv72ayb", 12652 "depends": ["BSgenome", "Biostrings", "BlandAltmanLeh", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "bamlss", "ggplot2", "scales"] 12653 }, 12654 "spillR": { 12655 "name": "spillR", 12656 "version": "1.6.0", 12657 "sha256": "1ac72p03xlzr4kg2wny7p17smrvprs6b5ng483x7369rsx7xf3di", 12658 "depends": ["CATALYST", "S4Vectors", "SummarizedExperiment", "dplyr", "ggplot2", "spatstat_univar", "tibble", "tidyr", "tidyselect"] 12659 }, 12660 "spkTools": { 12661 "name": "spkTools", 12662 "version": "1.66.0", 12663 "sha256": "1rgqfnicbv7sf5fggpdchkqq0x3z08qhrcrl469182dcmz09m966", 12664 "depends": ["Biobase", "RColorBrewer", "gtools"] 12665 }, 12666 "splatter": { 12667 "name": "splatter", 12668 "version": "1.34.0", 12669 "sha256": "0p9hr9p8b6n2q0mm1ihxydv53i5hn48pw03z4b50gz4d4w5nsqkv", 12670 "depends": ["BiocGenerics", "BiocParallel", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "crayon", "edgeR", "fitdistrplus", "locfit", "matrixStats", "rlang", "scuttle", "withr"] 12671 }, 12672 "splineTimeR": { 12673 "name": "splineTimeR", 12674 "version": "1.38.0", 12675 "sha256": "11yqzli5v6vgkwxj5m6aw4h5m3p3x65nzyn90rhyxfsly46zldkr", 12676 "depends": ["Biobase", "FIs", "GSEABase", "GeneNet", "gtools", "igraph", "limma", "longitudinal"] 12677 }, 12678 "splots": { 12679 "name": "splots", 12680 "version": "1.76.0", 12681 "sha256": "0b5n6gy87q1yg29a594avq2d7qssk0s3b33qd0ky62lb8innra4r", 12682 "depends": ["RColorBrewer"] 12683 }, 12684 "spoon": { 12685 "name": "spoon", 12686 "version": "1.6.0", 12687 "sha256": "145h823ax4hc8a9y8vsd1s4gli47kcb6hcxffa0wk989yb249zj9", 12688 "depends": ["BRISC", "BiocParallel", "Matrix", "SpatialExperiment", "SummarizedExperiment", "nnSVG", "scuttle"] 12689 }, 12690 "spqn": { 12691 "name": "spqn", 12692 "version": "1.22.0", 12693 "sha256": "1cj1b5zx5mb1mwi1apk8655hh76xjm6cr2wwrdn1df68z08pnspc", 12694 "depends": ["BiocGenerics", "SummarizedExperiment", "ggplot2", "ggridges", "matrixStats"] 12695 }, 12696 "squallms": { 12697 "name": "squallms", 12698 "version": "1.4.0", 12699 "sha256": "13v0cwxjrspfhpcnm3v99kfa99vpdxkyy2045k9rrig5xjszwvzy", 12700 "depends": ["MSnbase", "MsExperiment", "RaMS", "caret", "data_table", "dplyr", "ggplot2", "keys", "plotly", "shiny", "tibble", "tidyr", "xcms"] 12701 }, 12702 "srnadiff": { 12703 "name": "srnadiff", 12704 "version": "1.30.0", 12705 "sha256": "1b2xg8xmh00zsbnrhpl5mak52w3pmw67jnx57hkdm55kxdzhdjq3", 12706 "depends": ["BiocManager", "BiocParallel", "BiocStyle", "DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "Rcpp", "Rsamtools", "S4Vectors", "Seqinfo", "SummarizedExperiment", "edgeR", "rtracklayer"] 12707 }, 12708 "ssPATHS": { 12709 "name": "ssPATHS", 12710 "version": "1.24.0", 12711 "sha256": "1gn7j7hb030w9w0aqg9kd8i3dcanag73jjxvjm04ql4v0cvvclz2", 12712 "depends": ["MESS", "ROCR", "SummarizedExperiment", "dml"] 12713 }, 12714 "sscu": { 12715 "name": "sscu", 12716 "version": "2.40.0", 12717 "sha256": "0p12i809pxvikddpamr8a8ri765aw8w76q98wd0f0c8x44xdy46r", 12718 "depends": ["BiocGenerics", "Biostrings", "seqinr"] 12719 }, 12720 "ssize": { 12721 "name": "ssize", 12722 "version": "1.84.0", 12723 "sha256": "1z7yw4apg4j8as6ygf9dm8rgvjfvp67awks03hjw8a5x0ym7gv5j", 12724 "depends": ["gdata", "xtable"] 12725 }, 12726 "ssrch": { 12727 "name": "ssrch", 12728 "version": "1.26.0", 12729 "sha256": "1z94gq0d706c372zd7kmakwzxzjkdzdf7a4sjdd08q8yds973vrb", 12730 "depends": ["DT", "shiny"] 12731 }, 12732 "ssviz": { 12733 "name": "ssviz", 12734 "version": "1.44.0", 12735 "sha256": "0q029f4cgwa0jc0dcpz8v10779gwnz0c4ps6fls6miyxay5lkizw", 12736 "depends": ["Biostrings", "RColorBrewer", "Rsamtools", "ggplot2", "reshape"] 12737 }, 12738 "stJoincount": { 12739 "name": "stJoincount", 12740 "version": "1.12.0", 12741 "sha256": "1m2crwvr5nca9358q8mwj2i53lci7lyn553kbj9c1wj4f5wwi9jy", 12742 "depends": ["Seurat", "SpatialExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "magrittr", "pheatmap", "raster", "sp", "spdep"] 12743 }, 12744 "stPipe": { 12745 "name": "stPipe", 12746 "version": "1.0.0", 12747 "sha256": "0x20phlrv0mlyr9q7hs5pdz9vcm1lvh0qdjp3z6kry53l4cqql0n", 12748 "depends": ["DropletUtils", "Rcpp", "Rhdf5lib", "Rhtslib", "Rsubread", "Rtsne", "Seurat", "SeuratObject", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "basilisk", "data_table", "dplyr", "ggplot2", "pbmcapply", "reticulate", "rmarkdown", "scPipe", "shiny", "testthat", "umap", "yaml"] 12749 }, 12750 "stageR": { 12751 "name": "stageR", 12752 "version": "1.32.0", 12753 "sha256": "1jivk3an5dh7hc0k21mg0pldpyfjwby09bj9r9ji75r9fwp20s6m", 12754 "depends": ["SummarizedExperiment"] 12755 }, 12756 "standR": { 12757 "name": "standR", 12758 "version": "1.14.0", 12759 "sha256": "0w9p8lndd5daadw7q4yr812ww3npvmb9awjxwwkdjpy0qrkvm5ck", 12760 "depends": ["Biobase", "BiocGenerics", "RUVSeq", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "dplyr", "edgeR", "ggalluvial", "ggplot2", "limma", "mclustcomp", "patchwork", "readr", "rlang", "ruv", "tibble", "tidyr"] 12761 }, 12762 "statTarget": { 12763 "name": "statTarget", 12764 "version": "1.40.0", 12765 "sha256": "1ch2gah8bivamm78d3gqa9abr91290nb45d1gl84l82hi00lin7b", 12766 "depends": ["ROC", "impute", "pdist", "pls", "plyr", "randomForest", "rrcov"] 12767 }, 12768 "stepNorm": { 12769 "name": "stepNorm", 12770 "version": "1.82.0", 12771 "sha256": "1pab1ppdx3zj8s4j19yk54nmify91191q4mqf9b7y3kdv6m4kkhf", 12772 "depends": ["MASS", "marray"] 12773 }, 12774 "strandCheckR": { 12775 "name": "strandCheckR", 12776 "version": "1.28.0", 12777 "sha256": "1djwigg75shja0nrkh63pwaaigpawwisywzyk5wfrkv1g30jr8a4", 12778 "depends": ["BiocGenerics", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "TxDb_Hsapiens_UCSC_hg38_knownGene", "dplyr", "ggplot2", "gridExtra", "reshape2", "rlang", "stringr", "tidyselect"] 12779 }, 12780 "subSeq": { 12781 "name": "subSeq", 12782 "version": "1.40.0", 12783 "sha256": "1cyvjbhis1fc0qb9iskjggmik76bmjizb1mn7b3dkiqkdkhns96p", 12784 "depends": ["Biobase", "data_table", "digest", "dplyr", "ggplot2", "magrittr", "qvalue", "tidyr"] 12785 }, 12786 "supersigs": { 12787 "name": "supersigs", 12788 "version": "1.18.0", 12789 "sha256": "01iq5xss5xyj88bkpf3vhcb8rh55bkcgm388055wc9kqyh2c0qvv", 12790 "depends": ["Biostrings", "SummarizedExperiment", "assertthat", "caret", "dplyr", "rlang", "rsample", "tidyr"] 12791 }, 12792 "surfaltr": { 12793 "name": "surfaltr", 12794 "version": "1.16.0", 12795 "sha256": "0cx7qh51n57d6zwc4s589c3jc51l7rzrw8qhjhm197w9yyvsz0p1", 12796 "depends": ["Biostrings", "biomaRt", "dplyr", "ggplot2", "httr", "msa", "protr", "readr", "seqinr", "stringr", "testthat", "xml2"] 12797 }, 12798 "survClust": { 12799 "name": "survClust", 12800 "version": "1.4.0", 12801 "sha256": "0462yjzrdwlm4bvxyh2vpijjrphkva36v4mhv5014ifrgdvg7i6k", 12802 "depends": ["MultiAssayExperiment", "Rcpp", "pdist", "survival"] 12803 }, 12804 "survcomp": { 12805 "name": "survcomp", 12806 "version": "1.60.0", 12807 "sha256": "0fhi7kjcd26shx0qh1j8akcbiwyaxb5b7jzk1hyzmdqf4ffs98kw", 12808 "depends": ["KernSmooth", "SuppDists", "bootstrap", "ipred", "prodlim", "rmeta", "survival", "survivalROC"] 12809 }, 12810 "survtype": { 12811 "name": "survtype", 12812 "version": "1.26.0", 12813 "sha256": "1c63fn4m7cg0vgj1rxxgrfxx002m331dprzv2zkfpg0ip1k5dmkm", 12814 "depends": ["SummarizedExperiment", "clustvarsel", "pheatmap", "survival", "survminer"] 12815 }, 12816 "sva": { 12817 "name": "sva", 12818 "version": "3.58.0", 12819 "sha256": "0q2j31lf4bm9karlj0fnd04rxbi6h0dk5n3rcjcb4vd69aj05bfg", 12820 "depends": ["BiocParallel", "edgeR", "genefilter", "limma", "matrixStats", "mgcv"] 12821 }, 12822 "svaNUMT": { 12823 "name": "svaNUMT", 12824 "version": "1.16.0", 12825 "sha256": "00kxwi11s84sx7dfrsc40s52jg9izsyrxvl9x94qd4fdfxlg78as", 12826 "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "S4Vectors", "Seqinfo", "StructuralVariantAnnotation", "VariantAnnotation", "assertthat", "dplyr", "pwalign", "rlang", "rtracklayer", "stringr"] 12827 }, 12828 "svaRetro": { 12829 "name": "svaRetro", 12830 "version": "1.15.1", 12831 "sha256": "0cb1d9h35q72058if30k1fixairvrvra0k9lcarg8kalav5x7467", 12832 "depends": ["BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "S4Vectors", "Seqinfo", "StructuralVariantAnnotation", "VariantAnnotation", "assertthat", "dplyr", "rlang", "rtracklayer", "stringr"] 12833 }, 12834 "swfdr": { 12835 "name": "swfdr", 12836 "version": "1.36.0", 12837 "sha256": "132fdhnp78ns5d7g2q60lvax098bamnv2kz7rw5s2dk06fj2gdhi", 12838 "depends": [] 12839 }, 12840 "switchBox": { 12841 "name": "switchBox", 12842 "version": "1.46.0", 12843 "sha256": "1das904wcjx90spw7rzj0w2w8i070gf18150wliw61s0901yljba", 12844 "depends": ["gplots", "pROC"] 12845 }, 12846 "switchde": { 12847 "name": "switchde", 12848 "version": "1.36.0", 12849 "sha256": "0174ajkl30fkp9f85vbk7crfigaq0gcqwqykd2rz6cxg83znvpx6", 12850 "depends": ["SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2"] 12851 }, 12852 "synapsis": { 12853 "name": "synapsis", 12854 "version": "1.16.0", 12855 "sha256": "1b5shghlsiiga8vng4ijw3w0jbmnyx5bhk6rbf099h1603v9dyp7", 12856 "depends": ["EBImage"] 12857 }, 12858 "synergyfinder": { 12859 "name": "synergyfinder", 12860 "version": "3.18.0", 12861 "sha256": "1mdaksmhdq96bf64lq2jg7n94mgh5iaa071cx2wmf9iq0pamnzy9", 12862 "depends": ["SpatialExtremes", "dplyr", "drc", "furrr", "future", "ggforce", "ggplot2", "ggrepel", "gstat", "kriging", "lattice", "magrittr", "metR", "mice", "nleqslv", "pbapply", "plotly", "purrr", "reshape2", "sp", "stringr", "tidyr", "tidyverse", "vegan"] 12863 }, 12864 "synlet": { 12865 "name": "synlet", 12866 "version": "2.10.0", 12867 "sha256": "12l0g6684rjm8vrw1l5gzcdsp4217h68m5b6jjq8wpbzk89m1fif", 12868 "depends": ["RColorBrewer", "RankProd", "data_table", "ggplot2", "magrittr", "patchwork"] 12869 }, 12870 "syntenet": { 12871 "name": "syntenet", 12872 "version": "1.12.0", 12873 "sha256": "0znmvqxy70yypfpm3bfhz9jdrw1ihr8vlim8mh19cwpkmlm87rd2", 12874 "depends": ["BiocParallel", "Biostrings", "GenomicRanges", "RColorBrewer", "Rcpp", "ggnetwork", "ggplot2", "igraph", "intergraph", "pheatmap", "rlang", "testthat"] 12875 }, 12876 "systemPipeR": { 12877 "name": "systemPipeR", 12878 "version": "2.16.0", 12879 "sha256": "1mpwjz0r5cy2r5745b4splygg6jycfnfrqrca9vqic3bnpsrc6gf", 12880 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "crayon", "ggplot2", "htmlwidgets", "magrittr", "stringr", "yaml"] 12881 }, 12882 "systemPipeShiny": { 12883 "name": "systemPipeShiny", 12884 "version": "1.20.0", 12885 "sha256": "13a19n35gavrrnm8r0p7snl4cfjsb6nwhidyd5vv97bsj53dmvqw", 12886 "depends": ["DT", "R6", "RSQLite", "assertthat", "bsplus", "crayon", "dplyr", "drawer", "ggplot2", "glue", "htmltools", "magrittr", "openssl", "plotly", "rlang", "rstudioapi", "shiny", "shinyAce", "shinyFiles", "shinyWidgets", "shinydashboard", "shinydashboardPlus", "shinyjqui", "shinyjs", "shinytoastr", "spsComps", "spsUtil", "stringr", "styler", "tibble", "vroom", "yaml"] 12887 }, 12888 "systemPipeTools": { 12889 "name": "systemPipeTools", 12890 "version": "1.18.0", 12891 "sha256": "1r1h14v9wrdxq7vnjhss7zax5hxygv215hp2y7r5lgzjfsh349ff", 12892 "depends": ["DESeq2", "DT", "GGally", "Rtsne", "SummarizedExperiment", "ape", "dplyr", "ggplot2", "ggrepel", "ggtree", "glmpca", "magrittr", "pheatmap", "plotly", "tibble"] 12893 }, 12894 "tLOH": { 12895 "name": "tLOH", 12896 "version": "1.18.0", 12897 "sha256": "1qi4csdvwviz4dm9mdxigq8n0yp6axqzxi97d7dmp2hlyvz9y108", 12898 "depends": ["GenomicRanges", "MatrixGenerics", "VariantAnnotation", "bestNormalize", "data_table", "depmixS4", "dplyr", "ggplot2", "naniar", "purrr", "scales", "stringr"] 12899 }, 12900 "tRNA": { 12901 "name": "tRNA", 12902 "version": "1.28.0", 12903 "sha256": "1c8q4i0xmbl3dl7ylid6wzw46l961pnrfb5pbv2jn31k1qc3ikif", 12904 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "Modstrings", "S4Vectors", "Structstrings", "XVector", "ggplot2", "scales", "stringr"] 12905 }, 12906 "tRNAdbImport": { 12907 "name": "tRNAdbImport", 12908 "version": "1.28.0", 12909 "sha256": "1p3q1vy8hx2f96zjmwgkpzv0q5vvivi2p54blrx1i99mc6ady2vc", 12910 "depends": ["Biostrings", "GenomicRanges", "IRanges", "Modstrings", "S4Vectors", "Structstrings", "httr2", "stringr", "tRNA", "xml2"] 12911 }, 12912 "tRNAscanImport": { 12913 "name": "tRNAscanImport", 12914 "version": "1.30.0", 12915 "sha256": "1xdwmbgmcqya010kfy2d5wlih922wkb8al93x0bnsf3k2cjmwg5h", 12916 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "Seqinfo", "Structstrings", "XVector", "rtracklayer", "stringr", "tRNA"] 12917 }, 12918 "tRanslatome": { 12919 "name": "tRanslatome", 12920 "version": "1.48.0", 12921 "sha256": "01lmjdj2mf5j6zf007wgan4sfw6sjf89kd1wr6q08bscv3z7m2l7", 12922 "depends": ["Biobase", "DESeq2", "GOSemSim", "Heatplus", "RankProd", "anota", "edgeR", "gplots", "limma", "org_Hs_eg_db", "plotrix", "topGO"] 12923 }, 12924 "tadar": { 12925 "name": "tadar", 12926 "version": "1.8.0", 12927 "sha256": "1a5h8kayfcbghq4ifbala2hp2awx1vcn0ka20ff49c351x1s46j2", 12928 "depends": ["BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "MatrixGenerics", "Rsamtools", "S4Vectors", "Seqinfo", "VariantAnnotation", "ggplot2", "lifecycle", "rlang"] 12929 }, 12930 "tanggle": { 12931 "name": "tanggle", 12932 "version": "1.16.0", 12933 "sha256": "1w7cbz3jwxa2qhcvx9x0vbmsdxc0jsfdf1qp06h4p2lqg9kaqfvd", 12934 "depends": ["ape", "dplyr", "ggplot2", "ggtree", "phangorn", "rlang"] 12935 }, 12936 "target": { 12937 "name": "target", 12938 "version": "1.24.0", 12939 "sha256": "0ndb8vwvwfjl0wwjr783ijdlgaipa61lihzx0ja92s9p8lwyx4nr", 12940 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "matrixStats", "shiny"] 12941 }, 12942 "tenXplore": { 12943 "name": "tenXplore", 12944 "version": "1.32.0", 12945 "sha256": "08iayrc4415mcs0niy2bjs43zhni89d82p8h6bkj2zaaprivash5", 12946 "depends": ["AnnotationDbi", "BiocFileCache", "SummarizedExperiment", "matrixStats", "ontoProc", "org_Mm_eg_db", "shiny"] 12947 }, 12948 "terapadog": { 12949 "name": "terapadog", 12950 "version": "1.2.0", 12951 "sha256": "1fzjcrbxfdq4i7d42bajnd3v24ygb7ckm4mnycwbwcns15km2lxj", 12952 "depends": ["DESeq2", "KEGGREST", "biomaRt", "dplyr", "htmlwidgets", "plotly"] 12953 }, 12954 "ternarynet": { 12955 "name": "ternarynet", 12956 "version": "1.54.0", 12957 "sha256": "12fl6szk85h317xc5pxfw2szyz93005bvsnlwg5drars652r24fs", 12958 "depends": ["BiocParallel", "igraph"] 12959 }, 12960 "terraTCGAdata": { 12961 "name": "terraTCGAdata", 12962 "version": "1.14.0", 12963 "sha256": "0a8m9672w3wribzb7ah3cdcq1d610s1m26zq90jrwfy6glbd5jyq", 12964 "depends": ["AnVIL", "AnVILGCP", "BiocFileCache", "GenomicRanges", "MultiAssayExperiment", "RaggedExperiment", "S4Vectors", "TCGAutils", "dplyr", "readr", "tidyr"] 12965 }, 12966 "tidyCoverage": { 12967 "name": "tidyCoverage", 12968 "version": "1.6.0", 12969 "sha256": "01d50vh3vmfnzn55vpkvmjpkdw8q3qjll20bbhw5vbi5drcc08wk", 12970 "depends": ["BiocIO", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "cli", "dplyr", "fansi", "ggplot2", "pillar", "purrr", "rlang", "rtracklayer", "scales", "tidyr", "vctrs"] 12971 }, 12972 "tidyFlowCore": { 12973 "name": "tidyFlowCore", 12974 "version": "1.4.0", 12975 "sha256": "10gh3g5v9zpcky3i6hxy9kk648bcfpxxrjmfbfx44h1p7g62d4cs", 12976 "depends": ["Biobase", "dplyr", "flowCore", "ggplot2", "purrr", "rlang", "stringr", "tibble", "tidyr"] 12977 }, 12978 "tidySingleCellExperiment": { 12979 "name": "tidySingleCellExperiment", 12980 "version": "1.20.0", 12981 "sha256": "033bwfygp97jn8dp9blw303mg9d00q4k0ps6w9040hc1af91x92r", 12982 "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "cli", "dplyr", "ellipsis", "fansi", "ggplot2", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "rlang", "stringr", "tibble", "tidyr", "tidyselect", "ttservice", "vctrs"] 12983 }, 12984 "tidySpatialExperiment": { 12985 "name": "tidySpatialExperiment", 12986 "version": "1.5.1", 12987 "sha256": "0050syc762ff2mjx5sppl5f2v0qs9yhjigzxd7vp25kshm6jp5wg", 12988 "depends": ["BiocGenerics", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "cli", "dplyr", "fansi", "ggplot2", "lifecycle", "magick", "pillar", "pkgconfig", "plotly", "purrr", "rlang", "shiny", "stringr", "tibble", "tidySingleCellExperiment", "tidygate", "tidyr", "tidyselect", "ttservice", "vctrs"] 12989 }, 12990 "tidySummarizedExperiment": { 12991 "name": "tidySummarizedExperiment", 12992 "version": "1.20.0", 12993 "sha256": "02icipy5jzjfk3g17pbc6z5skg7w9hz13ddm4fln8w0fdsxij5xk", 12994 "depends": ["S4Vectors", "SummarizedExperiment", "cli", "dplyr", "ellipsis", "fansi", "ggplot2", "lifecycle", "magrittr", "pillar", "pkgconfig", "plyxp", "purrr", "rlang", "stringr", "tibble", "tidyr", "tidyselect", "ttservice", "vctrs"] 12995 }, 12996 "tidybulk": { 12997 "name": "tidybulk", 12998 "version": "2.0.0", 12999 "sha256": "19gzvnmraxssxcxw5jfg4j509ivmpacn1y6mczrk5c753sr6q2p0", 13000 "depends": ["GenomicRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "crayon", "dplyr", "ggplot2", "lifecycle", "magrittr", "purrr", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect", "ttservice"] 13001 }, 13002 "tidyomics": { 13003 "name": "tidyomics", 13004 "version": "1.6.0", 13005 "sha256": "1bwyhs3sv01qk3197mpv0sq0s0776a5p89lk8579axi9flyvgya2", 13006 "depends": ["cli", "plyranges", "purrr", "rlang", "stringr", "tidySingleCellExperiment", "tidySpatialExperiment", "tidySummarizedExperiment", "tidyseurat"] 13007 }, 13008 "tidysbml": { 13009 "name": "tidysbml", 13010 "version": "1.4.0", 13011 "sha256": "1c2yy1i5hfqa22znm7425zikdrsx9rzj07mncz19km9aaammrmm3", 13012 "depends": ["xml2"] 13013 }, 13014 "tigre": { 13015 "name": "tigre", 13016 "version": "1.64.0", 13017 "sha256": "1kha8gpy9gwissf8hl9jb39bj5bmkbb1zc063c8vdsw02fwacpdw", 13018 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "RSQLite", "annotate", "gplots"] 13019 }, 13020 "tilingArray": { 13021 "name": "tilingArray", 13022 "version": "1.88.0", 13023 "sha256": "069z6lvv238993dg66d6a6s6ql88410hxx2jccc64k9j090qj2rv", 13024 "depends": ["Biobase", "RColorBrewer", "affy", "genefilter", "pixmap", "strucchange", "vsn"] 13025 }, 13026 "timeOmics": { 13027 "name": "timeOmics", 13028 "version": "1.22.0", 13029 "sha256": "0xqsxmn9jg475sbg54dbhqqs63154pqplpn0676fx96i8prv85rf", 13030 "depends": ["checkmate", "dplyr", "ggplot2", "ggrepel", "lmtest", "magrittr", "mixOmics", "plyr", "purrr", "stringr", "tibble", "tidyr"] 13031 }, 13032 "timecourse": { 13033 "name": "timecourse", 13034 "version": "1.82.0", 13035 "sha256": "1zy6z2bhqzbkhn4y8fmf5jrn3qyvj4gjfhl1z1yj02xbc9xh6m1q", 13036 "depends": ["Biobase", "MASS", "limma", "marray"] 13037 }, 13038 "timescape": { 13039 "name": "timescape", 13040 "version": "1.34.0", 13041 "sha256": "0dlvr08k8dr7fw1igzkigpwwrn9iy8ca1wnvgca082jczlxgh19w", 13042 "depends": ["dplyr", "gtools", "htmlwidgets", "jsonlite", "stringr"] 13043 }, 13044 "tkWidgets": { 13045 "name": "tkWidgets", 13046 "version": "1.88.0", 13047 "sha256": "0y2zj1ikcdfk4n9ngh3d5k3jkbnqxx8pgp3mywbff6ijlnh3hvl9", 13048 "depends": ["DynDoc", "widgetTools"] 13049 }, 13050 "tomoda": { 13051 "name": "tomoda", 13052 "version": "1.20.0", 13053 "sha256": "148fgacd38kqm7vrlhlh5bjddngzr999zsd2hb9shnpfjlaz8prl", 13054 "depends": ["RColorBrewer", "Rtsne", "SummarizedExperiment", "ggplot2", "ggrepel", "reshape2", "umap"] 13055 }, 13056 "tomoseqr": { 13057 "name": "tomoseqr", 13058 "version": "1.14.0", 13059 "sha256": "1bbfbih0zq83051izdl2v9c218bqz6b3r13bn4xkg7g096588g4b", 13060 "depends": ["BiocFileCache", "animation", "dplyr", "ggplot2", "plotly", "purrr", "readr", "shiny", "stringr", "tibble"] 13061 }, 13062 "topGO": { 13063 "name": "topGO", 13064 "version": "2.62.0", 13065 "sha256": "1qg9534rnfvysgwg7dbnv1px75xi19din2jlyxivfw9fdz2k3jkb", 13066 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DBI", "GO_db", "SparseM", "graph", "lattice", "matrixStats"] 13067 }, 13068 "topconfects": { 13069 "name": "topconfects", 13070 "version": "1.26.0", 13071 "sha256": "1n27xg9s7ml8ys3mhb6m62rlh37f4n3g3v174vl5rjdwv3f21kaf", 13072 "depends": ["assertthat", "ggplot2", "scales"] 13073 }, 13074 "topdownr": { 13075 "name": "topdownr", 13076 "version": "1.32.0", 13077 "sha256": "0ari49mb87gqkrlgk0ar31i4k4b989li7nnpkzsn8163m873qwqy", 13078 "depends": ["Biobase", "BiocGenerics", "Biostrings", "MSnbase", "Matrix", "PSMatch", "ProtGenerics", "S4Vectors", "ggplot2", "mzR"] 13079 }, 13080 "tpSVG": { 13081 "name": "tpSVG", 13082 "version": "1.6.0", 13083 "sha256": "11fk4mipi0kql70mvys82pqfhzv5w4yphvv4b723i93xj54qgsba", 13084 "depends": ["BiocParallel", "MatrixGenerics", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "mgcv"] 13085 }, 13086 "trackViewer": { 13087 "name": "trackViewer", 13088 "version": "1.46.0", 13089 "sha256": "1asyrcdq65135f2s551s543gvwcb651xmcbn9p3z2rrj53v0xxq2", 13090 "depends": ["AnnotationDbi", "BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "InteractionSet", "Rsamtools", "S4Vectors", "Seqinfo", "grImport", "htmlwidgets", "rhdf5", "rtracklayer", "scales", "strawr", "txdbmaker"] 13091 }, 13092 "tracktables": { 13093 "name": "tracktables", 13094 "version": "1.44.0", 13095 "sha256": "0r2wgl0ammh794rgcll22y31l2988bq2gf7605xiq43vf1sgipv9", 13096 "depends": ["GenomicRanges", "IRanges", "RColorBrewer", "Rsamtools", "XML", "XVector", "stringr", "tractor_base"] 13097 }, 13098 "tradeSeq": { 13099 "name": "tradeSeq", 13100 "version": "1.24.0", 13101 "sha256": "1lyy5irrq4bqah9v8sff2mgfs5xa6sm62kxkbq0i0clnad9zhvj9", 13102 "depends": ["Biobase", "BiocParallel", "MASS", "Matrix", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "TrajectoryUtils", "edgeR", "ggplot2", "igraph", "magrittr", "matrixStats", "mgcv", "pbapply", "princurve", "slingshot", "tibble", "viridis"] 13103 }, 13104 "transcriptR": { 13105 "name": "transcriptR", 13106 "version": "1.37.0", 13107 "sha256": "18gxiwl1i5v10rxdprnpjylx57p2zfgpm5akb2vn7mzj24n4fhh3", 13108 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "caret", "chipseq", "e1071", "ggplot2", "pROC", "reshape2", "rtracklayer"] 13109 }, 13110 "transcriptogramer": { 13111 "name": "transcriptogramer", 13112 "version": "1.32.0", 13113 "sha256": "03p4h5n589aiin7zzlc8a2ma7sw0l0v61vnh0sd7n1ix9ahx94sb", 13114 "depends": ["RedeR", "biomaRt", "data_table", "doSNOW", "foreach", "ggplot2", "igraph", "limma", "progress", "snow", "tidyr", "topGO"] 13115 }, 13116 "transformGamPoi": { 13117 "name": "transformGamPoi", 13118 "version": "1.16.0", 13119 "sha256": "1r34723v0q39w693im6z77rpf4jradklzvxj0dlrzv4y6k9nrzy2", 13120 "depends": ["DelayedArray", "HDF5Array", "Matrix", "MatrixGenerics", "Rcpp", "SummarizedExperiment", "glmGamPoi"] 13121 }, 13122 "transite": { 13123 "name": "transite", 13124 "version": "1.28.0", 13125 "sha256": "070rfxna1qdk9vibci4kjjh8mpv9mhm66hnb6bgyncwxsn4v520a", 13126 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "Rcpp", "TFMPvalue", "dplyr", "ggplot2", "gridExtra", "scales", "stringr"] 13127 }, 13128 "transmogR": { 13129 "name": "transmogR", 13130 "version": "1.6.0", 13131 "sha256": "13pwks45wqia6zlbkn85rngzsnzr86d980hc48caafn59cj1b057", 13132 "depends": ["BSgenome", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo", "SummarizedExperiment", "VariantAnnotation", "data_table", "ggplot2", "jsonlite", "matrixStats", "patchwork", "scales"] 13133 }, 13134 "transomics2cytoscape": { 13135 "name": "transomics2cytoscape", 13136 "version": "1.20.0", 13137 "sha256": "1r6yr82s78vmfff5nsxmhc098s8y20ii9a4rfxxy0b3rv15bz0ry", 13138 "depends": ["KEGGREST", "RCy3", "dplyr", "pbapply", "purrr", "tibble"] 13139 }, 13140 "traseR": { 13141 "name": "traseR", 13142 "version": "1.40.0", 13143 "sha256": "1rwjfmliqihnbhybjk3svzpk02f80md6d8g8i51z03lnanjgca6f", 13144 "depends": ["BSgenome_Hsapiens_UCSC_hg19", "GenomicRanges", "IRanges"] 13145 }, 13146 "treeclimbR": { 13147 "name": "treeclimbR", 13148 "version": "1.6.0", 13149 "sha256": "0kgkyl1kz7my9gxf2sb2h1xpb1hqr6zvs6zrjgprsgwy17p1cj32", 13150 "depends": ["S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "ape", "diffcyt", "dirmult", "dplyr", "edgeR", "ggnewscale", "ggplot2", "ggtree", "rlang", "tibble", "tidyr", "viridis"] 13151 }, 13152 "treeio": { 13153 "name": "treeio", 13154 "version": "1.34.0", 13155 "sha256": "1hm8c1znf29cmprlsyfqaks56qqq034kmvnlfvb5x4r5b7drccqp", 13156 "depends": ["ape", "dplyr", "jsonlite", "magrittr", "rlang", "tibble", "tidytree", "yulab_utils"] 13157 }, 13158 "treekoR": { 13159 "name": "treekoR", 13160 "version": "1.18.0", 13161 "sha256": "1ljq7a265flysfz7g0225ab46gqpws66nvgpm9pq901g9bjjh3sp", 13162 "depends": ["SingleCellExperiment", "ape", "data_table", "diffcyt", "dplyr", "edgeR", "ggiraph", "ggplot2", "ggtree", "hopach", "lme4", "multcomp", "patchwork", "tidyr"] 13163 }, 13164 "tricycle": { 13165 "name": "tricycle", 13166 "version": "1.18.0", 13167 "sha256": "0iafaafqph9a1hjmgdzwjr8fn3cn98mfvy42i68kcbih0c4n25ib", 13168 "depends": ["AnnotationDbi", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "circular", "dplyr", "ggnewscale", "ggplot2", "scater", "scattermore"] 13169 }, 13170 "trio": { 13171 "name": "trio", 13172 "version": "3.48.0", 13173 "sha256": "02x86cf6ahs8cdb2gani83059h7ryldy4m1s8gsc7nqsv0ryg1pj", 13174 "depends": ["LogicReg", "data_table", "siggenes", "survival"] 13175 }, 13176 "triplex": { 13177 "name": "triplex", 13178 "version": "1.50.0", 13179 "sha256": "0q23akzzx374irjyj9sdvia46x626655rwccjqz2i2bak5azj87a", 13180 "depends": ["Biostrings", "GenomicRanges", "IRanges", "S4Vectors", "XVector"] 13181 }, 13182 "tripr": { 13183 "name": "tripr", 13184 "version": "1.16.0", 13185 "sha256": "0n384vfxasbxspwryllzy37kgjgsn92q6x0asr2b4k0hksdn74r8", 13186 "depends": ["DT", "RColorBrewer", "config", "data_table", "dplyr", "golem", "gridExtra", "plot3D", "plotly", "plyr", "shiny", "shinyBS", "shinyFiles", "shinyjs", "stringdist", "stringr", "vegan"] 13187 }, 13188 "ttgsea": { 13189 "name": "ttgsea", 13190 "version": "1.18.0", 13191 "sha256": "1pxpfmy7d0m1fq7mq6wl9p5kdnyqiyavfiqarmi66pyrqw375kyi", 13192 "depends": ["DiagrammeR", "data_table", "keras", "purrr", "stopwords", "text2vec", "textstem", "tm", "tokenizers"] 13193 }, 13194 "tweeDEseq": { 13195 "name": "tweeDEseq", 13196 "version": "1.56.0", 13197 "sha256": "0vfxidfpl23m32v685ykyck7bfnmwzrncq2h10qcak3w0jfis5pc", 13198 "depends": ["MASS", "Rcpp", "cqn", "edgeR", "limma"] 13199 }, 13200 "twilight": { 13201 "name": "twilight", 13202 "version": "1.86.0", 13203 "sha256": "0s01z7q645qs5900vnwkfgpzchwnwdb7yi72a3p2nnbbwhdk0yb3", 13204 "depends": ["Biobase"] 13205 }, 13206 "twoddpcr": { 13207 "name": "twoddpcr", 13208 "version": "1.34.0", 13209 "sha256": "18v73fxsy1xlflx89dzsph039j307x356dkizckmrjmmr1v3hzdk", 13210 "depends": ["RColorBrewer", "S4Vectors", "class", "ggplot2", "hexbin", "scales", "shiny"] 13211 }, 13212 "txcutr": { 13213 "name": "txcutr", 13214 "version": "1.16.0", 13215 "sha256": "14n4d74xlijf99nsmn6yj8q0nxx9gas8krkzmsmdpma232y2z791", 13216 "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "rtracklayer", "txdbmaker"] 13217 }, 13218 "txdbmaker": { 13219 "name": "txdbmaker", 13220 "version": "1.6.0", 13221 "sha256": "0rczknnbccc2vlbs0mkv89fqmr1myxjba12dvvyqfpnh7pcxfihp", 13222 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocIO", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RSQLite", "S4Vectors", "Seqinfo", "UCSC_utils", "biomaRt", "httr", "rjson", "rtracklayer"] 13223 }, 13224 "tximeta": { 13225 "name": "tximeta", 13226 "version": "1.28.0", 13227 "sha256": "0rpka083c8gw3crd1sp2vhlbk9rbyvnc6r5gnr55am73rp7dk3px", 13228 "depends": ["AnnotationDbi", "AnnotationHub", "BiocFileCache", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "Seqinfo", "SummarizedExperiment", "ensembldb", "jsonlite", "tibble", "txdbmaker", "tximport"] 13229 }, 13230 "tximport": { 13231 "name": "tximport", 13232 "version": "1.38.0", 13233 "sha256": "1f6c8ha6gym85z96azr6939gdvwg4a6p07mlp9d79181vqwr4ps0", 13234 "depends": [] 13235 }, 13236 "uSORT": { 13237 "name": "uSORT", 13238 "version": "1.36.0", 13239 "sha256": "05hnsslcviqzia3vr3q1a23mk7jdly56gn7agdlrscn99wd4w34y", 13240 "depends": ["Biobase", "BiocGenerics", "Matrix", "RANN", "RSpectra", "VGAM", "cluster", "fpc", "gplots", "igraph", "monocle", "plyr"] 13241 }, 13242 "uncoverappLib": { 13243 "name": "uncoverappLib", 13244 "version": "1.20.0", 13245 "sha256": "107rzv1q58mxhks8ggw4krghc2071fjf745zqcrysfmz6nr7byrx", 13246 "depends": ["BiocFileCache", "DT", "EnsDb_Hsapiens_v75", "EnsDb_Hsapiens_v86", "GenomicRanges", "Gviz", "Homo_sapiens", "OrganismDbi", "Rsamtools", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "condformat", "markdown", "openxlsx", "org_Hs_eg_db", "processx", "rappdirs", "rlist", "shiny", "shinyBS", "shinyWidgets", "shinycssloaders", "shinyjs", "stringr"] 13247 }, 13248 "unifiedWMWqPCR": { 13249 "name": "unifiedWMWqPCR", 13250 "version": "1.46.0", 13251 "sha256": "1djpgr4y4vcf96acqqzlwf33mysfmpwj82iyzibsw4xxi17qr1yn", 13252 "depends": ["BiocGenerics", "limma"] 13253 }, 13254 "universalmotif": { 13255 "name": "universalmotif", 13256 "version": "1.28.0", 13257 "sha256": "1vx95g37kw4nf297dgrbw7n83d94zzcjpy2bqs2c5wgi3bh3rfa6", 13258 "depends": ["BiocGenerics", "Biostrings", "IRanges", "MASS", "MatrixGenerics", "Rcpp", "RcppThread", "S4Vectors", "ggplot2", "rlang", "yaml"] 13259 }, 13260 "updateObject": { 13261 "name": "updateObject", 13262 "version": "1.14.0", 13263 "sha256": "1rwlai7zj7gr43nppf6qnkzjdpyhd3wxnba4r1n0pkgjgpy6qwzv", 13264 "depends": ["BiocGenerics", "S4Vectors", "digest"] 13265 }, 13266 "variancePartition": { 13267 "name": "variancePartition", 13268 "version": "1.40.0", 13269 "sha256": "0inwnrk6jppjfmsin7zjlfg250y7q7049x5nis2xqn559pfls37s", 13270 "depends": ["Biobase", "BiocParallel", "MASS", "Matrix", "Rdpack", "RhpcBLASctl", "aod", "corpcor", "fANCOVA", "ggplot2", "gplots", "gtools", "iterators", "limma", "lme4", "lmerTest", "matrixStats", "pbkrtest", "remaCor", "reshape2", "rlang", "scales"] 13271 }, 13272 "vbmp": { 13273 "name": "vbmp", 13274 "version": "1.78.0", 13275 "sha256": "0cnswf82mzb5i36p2asv73rxxjbmdzp0silqfpl3xvh7j8dwqmsw", 13276 "depends": [] 13277 }, 13278 "velociraptor": { 13279 "name": "velociraptor", 13280 "version": "1.20.0", 13281 "sha256": "11752daakbh8gzhg4sg7bcph5m9gl3a7x5vsg21hiplayh5vsw25", 13282 "depends": ["BiocGenerics", "BiocParallel", "BiocSingular", "DelayedArray", "Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "basilisk", "reticulate", "scuttle", "zellkonverter"] 13283 }, 13284 "veloviz": { 13285 "name": "veloviz", 13286 "version": "1.16.0", 13287 "sha256": "0gkvbcm1aj697fvb5yyw3hd7ysy7dbhz24xjqfnl8n0z3w3b8dvm", 13288 "depends": ["Matrix", "RSpectra", "Rcpp", "igraph", "mgcv"] 13289 }, 13290 "vidger": { 13291 "name": "vidger", 13292 "version": "1.30.0", 13293 "sha256": "0nhbc0n82xk4qdkmv3d6fsaf7rmwq2hshi68yba6z75vjshkpfpa", 13294 "depends": ["Biobase", "DESeq2", "GGally", "RColorBrewer", "SummarizedExperiment", "edgeR", "ggplot2", "ggrepel", "knitr", "rmarkdown", "scales", "tidyr"] 13295 }, 13296 "viper": { 13297 "name": "viper", 13298 "version": "1.44.0", 13299 "sha256": "1glm6xmbsppi0yhriyn44h32whjy004szn5bq5qmj4jdprqbj4yj", 13300 "depends": ["Biobase", "KernSmooth", "e1071", "mixtools"] 13301 }, 13302 "visiumStitched": { 13303 "name": "visiumStitched", 13304 "version": "1.2.0", 13305 "sha256": "1w41968mlfkc5gmdw3h3jzmirvlnbsarkqirj0j2l4f1fgx2lgs7", 13306 "depends": ["BiocBaseUtils", "BiocGenerics", "DropletUtils", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "clue", "dplyr", "imager", "pkgcond", "readr", "rjson", "spatialLIBD", "stringr", "tibble", "tidyr", "xml2"] 13307 }, 13308 "vissE": { 13309 "name": "vissE", 13310 "version": "1.18.0", 13311 "sha256": "1k7x0ihb34226xvq39v3hvknwybrwa0makdkq28zazfqlm1rk09g", 13312 "depends": ["GSEABase", "RColorBrewer", "ggforce", "ggplot2", "ggraph", "ggrepel", "ggwordcloud", "igraph", "msigdb", "plyr", "reshape2", "scales", "scico", "textstem", "tidygraph", "tm"] 13313 }, 13314 "vmrseq": { 13315 "name": "vmrseq", 13316 "version": "1.2.0", 13317 "sha256": "138x3i1agw0j4m6i5jpvmfdk3kh9shy4pwzm93h4y8468hpfanm4", 13318 "depends": ["BiocParallel", "DelayedArray", "GenomicRanges", "HDF5Array", "IRanges", "S4Vectors", "SummarizedExperiment", "bumphunter", "data_table", "devtools", "dplyr", "gamlss_dist", "ggplot2", "locfit", "recommenderlab", "tidyr"] 13319 }, 13320 "vsclust": { 13321 "name": "vsclust", 13322 "version": "1.12.0", 13323 "sha256": "0gnk0bd3nqzla5fbxpx3zd1612qzq84zpw7hsk2l0f3xgwl1zfr6", 13324 "depends": ["DOSE", "MultiAssayExperiment", "Rcpp", "clusterProfiler", "httr", "limma", "matrixStats", "qvalue", "shiny"] 13325 }, 13326 "vsn": { 13327 "name": "vsn", 13328 "version": "3.78.0", 13329 "sha256": "07skbp8pq3anmlsmw0zqc2lhsis6wg9a6vid2535iy5hpj3d0yv0", 13330 "depends": ["Biobase", "affy", "ggplot2", "lattice", "limma"] 13331 }, 13332 "vtpnet": { 13333 "name": "vtpnet", 13334 "version": "0.50.0", 13335 "sha256": "0zv8ci26f849k0rhh5c5hkgckymsp18hvqrh922sdf25c1khc8l7", 13336 "depends": ["GenomicRanges", "doParallel", "foreach", "graph", "gwascat"] 13337 }, 13338 "vulcan": { 13339 "name": "vulcan", 13340 "version": "1.32.0", 13341 "sha256": "1m52ai4z96b7kddg1c1cnm33h0w0hyg6r9ny5z8y1zipk6qja8cv", 13342 "depends": ["Biobase", "ChIPpeakAnno", "DESeq2", "DiffBind", "GenomicRanges", "S4Vectors", "TxDb_Hsapiens_UCSC_hg19_knownGene", "caTools", "csaw", "gplots", "locfit", "viper", "wordcloud", "zoo"] 13343 }, 13344 "waddR": { 13345 "name": "waddR", 13346 "version": "1.24.0", 13347 "sha256": "1x4kznzym44lsgn4hjfhqdqi04h8613qj7msvi3rwgnqi7qx0wg8", 13348 "depends": ["BiocFileCache", "BiocParallel", "Rcpp", "RcppArmadillo", "SingleCellExperiment", "arm", "eva"] 13349 }, 13350 "wateRmelon": { 13351 "name": "wateRmelon", 13352 "version": "2.16.0", 13353 "sha256": "1rp0jyg8g36lixy5zx1p3vxbqz95gq2cm0ky6zzc406ac0nwskpv", 13354 "depends": ["Biobase", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "ROC", "illuminaio", "limma", "lumi", "matrixStats", "methylumi"] 13355 }, 13356 "wavClusteR": { 13357 "name": "wavClusteR", 13358 "version": "2.44.0", 13359 "sha256": "1pid5gbq2jadrlkdk5s7pw90id4bdwnmi2pxi9h171mx591cmm23", 13360 "depends": ["BiocGenerics", "Biostrings", "GenomicFeatures", "GenomicRanges", "Hmisc", "IRanges", "Rsamtools", "S4Vectors", "foreach", "ggplot2", "mclust", "rtracklayer", "seqinr", "stringr"] 13361 }, 13362 "weaver": { 13363 "name": "weaver", 13364 "version": "1.76.0", 13365 "sha256": "0id7z8dxbdcsdmxc3hf91amy4y3s3iqyjsbr4vv01qdfb8y8dhsb", 13366 "depends": ["codetools", "digest"] 13367 }, 13368 "webbioc": { 13369 "name": "webbioc", 13370 "version": "1.82.0", 13371 "sha256": "0s3i6y01vvni3jlivsw708ylj3g2byx8agf72x48wwhlmp0v9gck", 13372 "depends": ["Biobase", "BiocManager", "affy", "annaffy", "gcrma", "multtest", "qvalue", "vsn"] 13373 }, 13374 "weitrix": { 13375 "name": "weitrix", 13376 "version": "1.22.0", 13377 "sha256": "00q7f6b1ib1kjnrmr3ps8cx2h5fc751zbl1kc7gh2wzg7gry9g5h", 13378 "depends": ["BiocGenerics", "BiocParallel", "Ckmeans_1d_dp", "DelayedArray", "DelayedMatrixStats", "RhpcBLASctl", "S4Vectors", "SummarizedExperiment", "assertthat", "dplyr", "ggplot2", "glm2", "limma", "purrr", "reshape2", "rlang", "scales", "topconfects"] 13379 }, 13380 "widgetTools": { 13381 "name": "widgetTools", 13382 "version": "1.88.0", 13383 "sha256": "0p6mqkjzwrnrbjjhbsg5bhbwm4wb2bmiqgbq6npmlrmcxz9xgvnw", 13384 "depends": [] 13385 }, 13386 "wiggleplotr": { 13387 "name": "wiggleplotr", 13388 "version": "1.34.0", 13389 "sha256": "0w4y9z4irzs03z6vmniwyz605048vxqdsb7q0yl9p45h13pm885h", 13390 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "assertthat", "cowplot", "dplyr", "ggplot2", "purrr", "rtracklayer"] 13391 }, 13392 "wpm": { 13393 "name": "wpm", 13394 "version": "1.20.0", 13395 "sha256": "04z1kgay2ix9hn434v9k9nja7jlvrz9ysrlajmzb1ipp51vw02q6", 13396 "depends": ["Biobase", "DT", "RColorBrewer", "SummarizedExperiment", "cli", "config", "dplyr", "ggplot2", "golem", "logging", "rlang", "shiny", "shinyWidgets", "shinycustomloader", "shinydashboard", "stringr"] 13397 }, 13398 "xCell2": { 13399 "name": "xCell2", 13400 "version": "1.2.0", 13401 "sha256": "1h7d93jh4iqs6bj8s9dc6apcm1178yl5yxngvi55wpj1h5hi438z", 13402 "depends": ["AnnotationHub", "BiocParallel", "Matrix", "Rfast", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "magrittr", "minpack_lm", "ontologyIndex", "pracma", "progress", "quadprog", "readr", "singscore", "tibble"] 13403 }, 13404 "xcms": { 13405 "name": "xcms", 13406 "version": "4.8.0", 13407 "sha256": "1d2p1hxa36423209cajl6b62rn7d1j0hf8s32p88yfxfv2rbswb8", 13408 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "IRanges", "MSnbase", "MassSpecWavelet", "MetaboCoreUtils", "MsCoreUtils", "MsExperiment", "MsFeatures", "ProtGenerics", "RColorBrewer", "S4Vectors", "Spectra", "SummarizedExperiment", "data_table", "lattice", "mzR", "progress"] 13409 }, 13410 "xcore": { 13411 "name": "xcore", 13412 "version": "1.14.0", 13413 "sha256": "0ks6ki009604pnmb49yiyi7lqdx8wgmpxr4jqs60ik28pb5sgwv6", 13414 "depends": ["DelayedArray", "GenomicRanges", "IRanges", "Matrix", "MultiAssayExperiment", "S4Vectors", "edgeR", "foreach", "glmnet", "iterators", "magrittr"] 13415 }, 13416 "xenLite": { 13417 "name": "xenLite", 13418 "version": "1.4.0", 13419 "sha256": "0fhl2lz68crvpb104r25pdwcvg567qxhsqkm941qxxv8inr08nmi", 13420 "depends": ["BiocFileCache", "EBImage", "HDF5Array", "Matrix", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "TENxIO", "arrow", "dplyr", "ggplot2", "shiny"] 13421 }, 13422 "xmapbridge": { 13423 "name": "xmapbridge", 13424 "version": "1.68.0", 13425 "sha256": "19f6wc6z42c978rd0pgg5kfs4b1bnnb0ywyc517wby6mqmhlgwai", 13426 "depends": [] 13427 }, 13428 "yamss": { 13429 "name": "yamss", 13430 "version": "1.36.0", 13431 "sha256": "0dixb373yx3jrmy9mm4z5mgqi37f271kv0fsj6a0mqd51429kacw", 13432 "depends": ["BiocGenerics", "EBImage", "IRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "data_table", "limma", "mzR"] 13433 }, 13434 "yarn": { 13435 "name": "yarn", 13436 "version": "1.36.0", 13437 "sha256": "1cv5mmzfqbgyzly9dbr3rxqgg5zk3vap0g3rjvh1f72rslv5fyj0", 13438 "depends": ["Biobase", "RColorBrewer", "biomaRt", "downloader", "edgeR", "gplots", "limma", "matrixStats", "preprocessCore", "quantro", "readr"] 13439 }, 13440 "zFPKM": { 13441 "name": "zFPKM", 13442 "version": "1.32.0", 13443 "sha256": "1lrj0pj966mq0vcj76qy9f82kfvv9spjgd90ipbfdnrvswcka53c", 13444 "depends": ["SummarizedExperiment", "checkmate", "dplyr", "ggplot2", "tidyr"] 13445 }, 13446 "zellkonverter": { 13447 "name": "zellkonverter", 13448 "version": "1.20.0", 13449 "sha256": "1w9kkx5qxskkxmq5y0x58pim5n9i4hms5mhm6y2n58qd1ja2qap2", 13450 "depends": ["DelayedArray", "Matrix", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "basilisk", "cli", "reticulate"] 13451 }, 13452 "zenith": { 13453 "name": "zenith", 13454 "version": "1.12.0", 13455 "sha256": "02dm4gi996qb3v09915zg0b4ibakjv5gmv2p39i1x185y2rbjmr9", 13456 "depends": ["EnrichmentBrowser", "GSEABase", "Rdpack", "Rfast", "dplyr", "ggplot2", "limma", "msigdbr", "progress", "reshape2", "tidyr", "variancePartition"] 13457 }, 13458 "zinbwave": { 13459 "name": "zinbwave", 13460 "version": "1.32.0", 13461 "sha256": "022pngsmgbkjgr7yp08pqhc83qbv42hdvjj47s4dfzhd6zyz301s", 13462 "depends": ["BiocParallel", "Matrix", "SingleCellExperiment", "SummarizedExperiment", "edgeR", "genefilter", "softImpute"] 13463 }, 13464 "zitools": { 13465 "name": "zitools", 13466 "version": "1.4.0", 13467 "sha256": "01mgf9m4080ws92zbdgxg28qlh9ly83nqa78x20kwhci3x95xy88", 13468 "depends": ["BiocGenerics", "DESeq2", "MatrixGenerics", "RColorBrewer", "SummarizedExperiment", "VGAM", "dplyr", "ggplot2", "magrittr", "matrixStats", "phyloseq", "pscl", "reshape2", "tibble", "tidyr"] 13469 }, 13470 "ABAEnrichment": { 13471 "name": "ABAEnrichment", 13472 "version": "1.2.2", 13473 "sha256": "0hmxxp12w67lp1g1djzlxffwlx32mnd1wbmz1hmv7y7z6h6ichvq", 13474 "depends": ["ABAData", "Rcpp", "gplots"], 13475 "broken": true 13476 }, 13477 "ALPS": { 13478 "name": "ALPS", 13479 "version": "1.5.0", 13480 "sha256": "1aydvzc6x0871iasij68xqdlhjyg69qbqxm0qh1q52w8gj2nyq3p", 13481 "depends": ["assertthat", "BiocParallel", "ChIPseeker", "corrplot", "data_table", "dplyr", "genefilter", "GenomicRanges", "GGally", "gghalves", "ggplot2", "ggseqlogo", "Gviz", "magrittr", "org_Hs_eg_db", "plyr", "reshape2", "rtracklayer", "stringr", "tibble", "tidyr", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene"], 13482 "broken": true 13483 }, 13484 "APAlyzer": { 13485 "name": "APAlyzer", 13486 "version": "1.22.0", 13487 "sha256": "00a3barcm8yr4q7c9irpmg5v6v8ybzb2ww9mb1r7fdkg0kpj6dj9", 13488 "depends": ["DESeq2", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "HybridMTest", "Rsamtools", "Rsubread", "SummarizedExperiment", "VariantAnnotation", "dplyr", "ggplot2", "ggrepel", "repmis", "rtracklayer", "tidyr"], 13489 "broken": true 13490 }, 13491 "ASpediaFI": { 13492 "name": "ASpediaFI", 13493 "version": "1.11.0", 13494 "sha256": "13jny6ca8hdf269z37baaggfs7jss00ln09apn42pj411g3p7nms", 13495 "depends": ["BiocParallel", "biomaRt", "dplyr", "DRaWR", "e1071", "fgsea", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "Gviz", "igraph", "IRanges", "IVAS", "limma", "Matrix", "reshape2", "ROCR", "Rsamtools", "rtracklayer", "S4Vectors", "scales", "SummarizedExperiment"], 13496 "broken": true 13497 }, 13498 "ATACCoGAPS": { 13499 "name": "ATACCoGAPS", 13500 "version": "1.6.0", 13501 "sha256": "09h32q9y7z65ck33rwqzw2wkl8l6016s0sdkhf2g094yxhkz26rh", 13502 "depends": ["BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Mmusculus_UCSC_mm10", "CoGAPS", "GeneOverlap", "GenomicFeatures", "GenomicRanges", "Homo_sapiens", "IRanges", "JASPAR2016", "Mus_musculus", "TFBSTools", "chromVAR", "dplyr", "fgsea", "gplots", "gtools", "motifmatchr", "msigdbr", "projectR", "rGREAT", "stringr", "tidyverse"], 13503 "broken": true 13504 }, 13505 "AffyCompatible": { 13506 "name": "AffyCompatible", 13507 "version": "1.30.0", 13508 "sha256": "1qw741j4d9b7bczjz3s72a9d0dcxbh5a2raak3ggwmz72p53axfz", 13509 "depends": ["Biostrings", "RCurl", "XML"], 13510 "broken": true 13511 }, 13512 "AffyExpress": { 13513 "name": "AffyExpress", 13514 "version": "1.36.0", 13515 "sha256": "186gc8c3bj070zvwyy4vz44wx1r85bbmil78b6m9kvwp6q1856d7", 13516 "depends": ["affy", "limma"], 13517 "broken": true 13518 }, 13519 "AffyTiling": { 13520 "name": "AffyTiling", 13521 "version": "1.28.0", 13522 "sha256": "08n1w64yk1pxb9d8dpa86y3mqxrsvyq0gsfzlsqg6fz8jz497fhr", 13523 "depends": ["affxparser", "affy", "preprocessCore"], 13524 "broken": true 13525 }, 13526 "AnalysisPageServer": { 13527 "name": "AnalysisPageServer", 13528 "version": "1.4.1", 13529 "sha256": "0zq0h9abswvhkpgb6f966rhgj7lh02aykq88fphxfv9zzkjfxbjp", 13530 "depends": ["Biobase", "graph", "log4r", "rjson"], 13531 "broken": true 13532 }, 13533 "AneuFinder": { 13534 "name": "AneuFinder", 13535 "version": "1.35.0", 13536 "sha256": "0zx0brvcyi9id7xli9h5nk9an7j46p7zgjj3qmwr3jm4b95qahpl", 13537 "depends": ["AneuFinderData", "BiocGenerics", "Biostrings", "DNAcopy", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "bamsignals", "cowplot", "doParallel", "ecp", "foreach", "ggdendro", "ggplot2", "ggrepel", "mclust", "reshape2"], 13538 "broken": true 13539 }, 13540 "AnnotationFuncs": { 13541 "name": "AnnotationFuncs", 13542 "version": "1.20.0", 13543 "sha256": "03rznpbsgq3pdh0id35vp8984f57ws2jpb0cww1qxglf967gy028", 13544 "depends": ["AnnotationDbi"], 13545 "broken": true 13546 }, 13547 "ArrayExpressHTS": { 13548 "name": "ArrayExpressHTS", 13549 "version": "1.20.0", 13550 "sha256": "00a5h3nwwhi9phrys2gj0ba8a24iqxk09licb0jn1qzdz9mrfxmq", 13551 "depends": ["Biobase", "BiocGenerics", "Biostrings", "DESeq", "GenomicRanges", "Hmisc", "IRanges", "R2HTML", "RColorBrewer", "Rsamtools", "ShortRead", "XML", "biomaRt", "bitops", "edgeR", "rJava", "sampling", "sendmailR", "snow", "svMisc"], 13552 "broken": true 13553 }, 13554 "ArrayTV": { 13555 "name": "ArrayTV", 13556 "version": "1.8.0", 13557 "sha256": "0ny5x2w0n3di5wzywfngsfdxaciczs24cnbvk75mv6hf4bdwfp74", 13558 "depends": ["DNAcopy", "foreach", "oligoClasses"], 13559 "broken": true 13560 }, 13561 "ArrayTools": { 13562 "name": "ArrayTools", 13563 "version": "1.30.0", 13564 "sha256": "168llqk8w1b54xy0ijg0m8mzcwggawkdr4s7abi2fv4q5007s1jv", 13565 "depends": ["Biobase", "affy", "limma", "xtable"], 13566 "broken": true 13567 }, 13568 "AtlasRDF": { 13569 "name": "AtlasRDF", 13570 "version": "1.6.0", 13571 "sha256": "16hgw47px7ig6hrm90y5nzy3dgdfm5my58bli20aj6dhnh2yvhxd", 13572 "depends": ["hash"], 13573 "broken": true 13574 }, 13575 "Autotuner": { 13576 "name": "Autotuner", 13577 "version": "1.7.0", 13578 "sha256": "0k07gs6bnxs0894iqi1lhk96mifjcdf68bv4q9fjv50nzqpzqd8l", 13579 "depends": ["assertthat", "Biobase", "cluster", "entropy", "MSnbase", "mzR", "RColorBrewer", "scales"], 13580 "broken": true 13581 }, 13582 "BAC": { 13583 "name": "BAC", 13584 "version": "1.30.0", 13585 "sha256": "1yrw01m8fd54v352pcb7904f8wi3il83nx8ywf6m968x33y2npxn", 13586 "depends": [], 13587 "broken": true 13588 }, 13589 "BDMMAcorrect": { 13590 "name": "BDMMAcorrect", 13591 "version": "1.18.1", 13592 "sha256": "17lsgl5mczfk2flkrclxhsqkkpr6mncccywm68l0z02pi5xhd8j7", 13593 "depends": ["ape", "ellipse", "ggplot2", "Rcpp", "RcppArmadillo", "RcppEigen", "SummarizedExperiment", "vegan"], 13594 "broken": true 13595 }, 13596 "BEARscc": { 13597 "name": "BEARscc", 13598 "version": "1.24.0", 13599 "sha256": "0f66pbhf4fz66021k7f6rlwzxdikznbhjqqpxwrj07yg65q5sd1l", 13600 "depends": ["SingleCellExperiment", "data_table", "ggplot2"], 13601 "broken": true 13602 }, 13603 "BGmix": { 13604 "name": "BGmix", 13605 "version": "1.30.0", 13606 "sha256": "1ii0cvqpz7ai779r4hx8yimsx69ln1f7qlw7jvp3k606z52kqkp2", 13607 "depends": ["KernSmooth"], 13608 "broken": true 13609 }, 13610 "BHC": { 13611 "name": "BHC", 13612 "version": "1.22.0", 13613 "sha256": "0m8w4b3ihnmvccy32nwvgzwn7k9i018ydw8iz19b6kz5r5c89q17", 13614 "depends": [], 13615 "broken": true 13616 }, 13617 "BPRMeth": { 13618 "name": "BPRMeth", 13619 "version": "1.34.0", 13620 "sha256": "0p06wjxmhfq3nyz1cwj0ghl3rnwd9lkhgzrndzgxb2a9l6v74w2h", 13621 "depends": ["BiocStyle", "GenomicRanges", "IRanges", "MASS", "Rcpp", "RcppArmadillo", "S4Vectors", "assertthat", "cowplot", "data_table", "doParallel", "e1071", "earth", "foreach", "ggplot2", "kernlab", "magrittr", "matrixcalc", "mvtnorm", "randomForest", "truncnorm"], 13622 "broken": true 13623 }, 13624 "BRGenomics": { 13625 "name": "BRGenomics", 13626 "version": "1.14.1", 13627 "sha256": "09kpb9jn84np1z8k72ngsbd0xx6v0x3kcl738wizr64w0j9zhlla", 13628 "depends": ["DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "rtracklayer", "S4Vectors", "SummarizedExperiment"], 13629 "broken": true 13630 }, 13631 "BayesPeak": { 13632 "name": "BayesPeak", 13633 "version": "1.22.0", 13634 "sha256": "1jmn8p461rmgjarf4rlhyqzrjg8xkpq56rlrk6964kqxp6jkh8bi", 13635 "depends": ["IRanges"], 13636 "broken": true 13637 }, 13638 "BiGGR": { 13639 "name": "BiGGR", 13640 "version": "1.44.0", 13641 "sha256": "1awdwwg54cfnsn8kp0lw6a7c3mgix024ry7mxn9vb5xq4hp1gflb", 13642 "depends": ["hyperdraw", "hypergraph", "limSolve", "rsbml", "stringr"], 13643 "broken": true 13644 }, 13645 "BioMM": { 13646 "name": "BioMM", 13647 "version": "1.15.0", 13648 "sha256": "01lfw0npcclcyqqh2xkhjq9jw0irbk13fsj5y1b3rz1amzzngg6p", 13649 "depends": ["BiocParallel", "CMplot", "e1071", "ggplot2", "glmnet", "imager", "lattice", "nsprcomp", "precrec", "ranger", "rms", "topGO", "vioplot", "xlsx"], 13650 "broken": true 13651 }, 13652 "BioNetStat": { 13653 "name": "BioNetStat", 13654 "version": "1.22.0", 13655 "sha256": "1rbb36v64b9xbk2dsf6wsyrhwwbkysrj8fp1g22y3gisdk170sg8", 13656 "depends": ["BiocParallel", "DT", "ggplot2", "Hmisc", "igraph", "knitr", "markdown", "pathview", "pheatmap", "plyr", "psych", "RColorBrewer", "RJSONIO", "rmarkdown", "shiny", "shinyBS", "whisker", "yaml"], 13657 "broken": true 13658 }, 13659 "BioPlex": { 13660 "name": "BioPlex", 13661 "version": "1.2.3", 13662 "sha256": "0cn0x6ij2a3xy61bq0qy5amp0ipj4r4shh7g0vlwbkrclj9w347r", 13663 "depends": ["BiocFileCache", "GenomeInfoDb", "GenomicRanges", "GEOquery", "graph", "SummarizedExperiment"], 13664 "broken": true 13665 }, 13666 "BioSeqClass": { 13667 "name": "BioSeqClass", 13668 "version": "1.28.0", 13669 "sha256": "0pv63d57hck04dpha20pzyzz7przzvi536nmgnsig5zw16lis4f2", 13670 "depends": ["Biobase", "Biostrings", "class", "e1071", "foreign", "ipred", "klaR", "nnet", "party", "randomForest", "rpart", "scatterplot3d", "tree"], 13671 "broken": true 13672 }, 13673 "BiocCaseStudies": { 13674 "name": "BiocCaseStudies", 13675 "version": "1.32.0", 13676 "sha256": "0wn3a01l6d62prrncmy22dx4nqsgzq3lw24ybf676ghrmjaygmyc", 13677 "depends": ["Biobase"], 13678 "broken": true 13679 }, 13680 "BiocDockerManager": { 13681 "name": "BiocDockerManager", 13682 "version": "1.11.0", 13683 "sha256": "0w393f14i253pnk0jzf2ci4g5cnxshwdjmix2r8arlnadh7spjyk", 13684 "depends": ["dplyr", "httr", "memoise", "readr", "whisker"], 13685 "broken": true 13686 }, 13687 "BiocInstaller": { 13688 "name": "BiocInstaller", 13689 "version": "1.20.3", 13690 "sha256": "0hjfhzbpxr7sfxac46ihklq0l7gkglrp7qi48vcp1s7xapnikblr", 13691 "depends": [], 13692 "broken": true 13693 }, 13694 "BiocOncoTK": { 13695 "name": "BiocOncoTK", 13696 "version": "1.24.0", 13697 "sha256": "0h4cr7lrmbyx7kdj81s7ff75svr01rvzn54svqi93vjilawmpbm3", 13698 "depends": ["ComplexHeatmap", "DBI", "DT", "GenomicFeatures", "GenomicRanges", "IRanges", "MASS", "Rgraphviz", "S4Vectors", "SummarizedExperiment", "bigrquery", "car", "curatedTCGAData", "dplyr", "ggplot2", "ggpubr", "graph", "httr", "magrittr", "plyr", "rjson", "scales", "shiny"], 13699 "broken": true 13700 }, 13701 "BitSeq": { 13702 "name": "BitSeq", 13703 "version": "1.14.0", 13704 "sha256": "1q58za8jd96bk2wxy7np0b7lar3v0pk6ll833k10x1b260rvpgbp", 13705 "depends": ["IRanges", "Rsamtools", "S4Vectors", "zlibbioc"], 13706 "broken": true 13707 }, 13708 "BrainSABER": { 13709 "name": "BrainSABER", 13710 "version": "1.8.0", 13711 "sha256": "1nxcjvaip7pp387bhdc2pmjai3chib1n63ig0cslhppzzjp2y6jd", 13712 "depends": ["BiocFileCache", "biomaRt", "data_table", "lsa", "S4Vectors", "shiny", "SummarizedExperiment"], 13713 "broken": true 13714 }, 13715 "BrainStars": { 13716 "name": "BrainStars", 13717 "version": "1.14.0", 13718 "sha256": "0r6jd6h48c15sg655079lwr9v1gl79wk8773w2q9fyfmakhj15vx", 13719 "depends": ["Biobase", "RCurl", "RJSONIO"], 13720 "broken": true 13721 }, 13722 "BrowserVizDemo": { 13723 "name": "BrowserVizDemo", 13724 "version": "1.2.3", 13725 "sha256": "1pj9b0nhkrc3bcs36dpm2hy9lsfp2xwnrlf99b9v6n96ijki8bg9", 13726 "depends": ["BiocGenerics", "BrowserViz", "httpuv", "jsonlite"], 13727 "broken": true 13728 }, 13729 "BubbleTree": { 13730 "name": "BubbleTree", 13731 "version": "2.38.0", 13732 "sha256": "1h3wyp9f554zlf4ah6dqgb1c26bkx1ks2q709hz3krchgzv3pinn", 13733 "depends": ["Biobase", "BiocGenerics", "BiocStyle", "GenomicRanges", "IRanges", "RColorBrewer", "WriteXLS", "biovizBase", "dplyr", "e1071", "ggplot2", "gridExtra", "gtable", "gtools", "limma", "magrittr", "plyr"], 13734 "broken": true 13735 }, 13736 "CALIB": { 13737 "name": "CALIB", 13738 "version": "1.36.0", 13739 "sha256": "1b21f0zg4czhk4pbd3c3vbl0p4qpw0l4wg17lm1gw4b6d6ml7jsb", 13740 "depends": ["limma"], 13741 "broken": true 13742 }, 13743 "CAnD": { 13744 "name": "CAnD", 13745 "version": "1.2.1", 13746 "sha256": "0ncpa81ac6dzkhqnr56i4nzzipsmzy44n71z6sdhpa39rgdar2a7", 13747 "depends": ["ggplot2", "reshape"], 13748 "broken": true 13749 }, 13750 "CBEA": { 13751 "name": "CBEA", 13752 "version": "1.6.0", 13753 "sha256": "1mbd62wakjn9pwhy2q2hfxkx09ny577a4j6lssnjj65jb3s7gjr6", 13754 "depends": ["BiocParallel", "BiocSet", "Rcpp", "SummarizedExperiment", "TreeSummarizedExperiment", "dplyr", "fitdistrplus", "generics", "glue", "goftest", "lmom", "magrittr", "mixtools", "rlang", "tibble", "tidyr"], 13755 "broken": true 13756 }, 13757 "CINdex": { 13758 "name": "CINdex", 13759 "version": "1.36.0", 13760 "sha256": "1cdmmnyxsrzlnsp15i8b072dfdsglql89ss1ddcwh4jyg8svwakl", 13761 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "bitops", "dplyr", "gplots", "gridExtra", "png", "som", "stringr"], 13762 "broken": true 13763 }, 13764 "CNPBayes": { 13765 "name": "CNPBayes", 13766 "version": "1.0.0", 13767 "sha256": "06jw9xi0q5slh1xghgj1js5bn1gsmpag0w84cxa7qf5ls1bw4xp6", 13768 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "Rcpp", "S4Vectors", "combinat", "foreach", "gtools", "matrixStats", "oligoClasses"], 13769 "broken": true 13770 }, 13771 "CNVgears": { 13772 "name": "CNVgears", 13773 "version": "1.8.0", 13774 "sha256": "1p7dxzkna3czkpsidj586hfwhymrjwvjr6q5f2pq7zlmpn6f8svx", 13775 "depends": ["data_table", "ggplot2"], 13776 "broken": true 13777 }, 13778 "CNVtools": { 13779 "name": "CNVtools", 13780 "version": "1.64.0", 13781 "sha256": "1sm28sl7ghcfrgjd0d741zfy21r6vxkhj8cn510z95aa49icpd8j", 13782 "depends": ["survival"], 13783 "broken": true 13784 }, 13785 "COHCAP": { 13786 "name": "COHCAP", 13787 "version": "1.8.0", 13788 "sha256": "1lak57k8b8jcd21wajr1ivi1sml73fsvb6jbdz6nxgjbq7al1hgk", 13789 "depends": ["COHCAPanno", "WriteXLS"], 13790 "broken": true 13791 }, 13792 "CORREP": { 13793 "name": "CORREP", 13794 "version": "1.36.0", 13795 "sha256": "0hjkwl2mf173mfdrziiadf5hacz6j67skizch44rxc2kfj7sbhyb", 13796 "depends": ["e1071"], 13797 "broken": true 13798 }, 13799 "CRISPRball": { 13800 "name": "CRISPRball", 13801 "version": "1.4.0", 13802 "sha256": "0y1hqb6jb356qff3jclab47jkf8i65qdva3idixi20y9m009q5s8", 13803 "depends": ["ComplexHeatmap", "DT", "InteractiveComplexHeatmap", "PCAtools", "circlize", "colourpicker", "dittoSeq", "ggplot2", "htmlwidgets", "matrixStats", "plotly", "shiny", "shinyBS", "shinyWidgets", "shinycssloaders", "shinyjqui", "shinyjs"], 13804 "broken": true 13805 }, 13806 "CSSP": { 13807 "name": "CSSP", 13808 "version": "1.8.0", 13809 "sha256": "05x0agbcpns8s3vmbs7ygdny249vcahzk7sqv50nz39ap2c7i309", 13810 "depends": [], 13811 "broken": true 13812 }, 13813 "CancerInSilico": { 13814 "name": "CancerInSilico", 13815 "version": "2.18.0", 13816 "sha256": "0szbz88wnr3dbf7k9bhihv6hkr29gsp9vrllr201wx5qfzl2gncy", 13817 "depends": ["BH", "Rcpp"], 13818 "broken": true 13819 }, 13820 "CancerMutationAnalysis": { 13821 "name": "CancerMutationAnalysis", 13822 "version": "1.13.0", 13823 "sha256": "0c3yjscd1jlgfl869vnv37qdb0y5gicnja1why9ws95qqgmij6zl", 13824 "depends": ["AnnotationDbi", "limma", "qvalue"], 13825 "broken": true 13826 }, 13827 "CancerSubtypes": { 13828 "name": "CancerSubtypes", 13829 "version": "1.26.0", 13830 "sha256": "06lw7b43fwh554870w71i676q6gm6kx53580cgg17a7prdjndkmr", 13831 "depends": ["cluster", "ConsensusClusterPlus", "impute", "limma", "NMF", "sigclust", "survival"], 13832 "broken": true 13833 }, 13834 "CellScore": { 13835 "name": "CellScore", 13836 "version": "1.27.0", 13837 "sha256": "11lhb46d5w3fq8qhlmap7wfirkpdnr6bqdpdarwxirrp076znvi2", 13838 "depends": ["Biobase", "RColorBrewer", "SummarizedExperiment", "gplots", "lsa", "squash"], 13839 "broken": true 13840 }, 13841 "CellaRepertorium": { 13842 "name": "CellaRepertorium", 13843 "version": "1.12.0", 13844 "sha256": "0k9sxh0b9g2841zpkbmcc65v0kfyv1i6sxzdmbr49nzzm27xlbh2", 13845 "depends": ["BiocGenerics", "Biostrings", "dplyr", "forcats", "generics", "glue", "Matrix", "progress", "purrr", "Rcpp", "reshape2", "rlang", "S4Vectors", "stringr", "tibble", "tidyr"], 13846 "broken": true 13847 }, 13848 "ChIC": { 13849 "name": "ChIC", 13850 "version": "1.19.0", 13851 "sha256": "0zbmhixxn3skn8csz93fyyfamz1n3gzjzb2caw8ybi2cysgzz5ys", 13852 "depends": ["BiocGenerics", "caret", "caTools", "ChIC_data", "genomeIntervals", "GenomicRanges", "IRanges", "progress", "randomForest", "Rsamtools", "S4Vectors"], 13853 "broken": true 13854 }, 13855 "ChIPQC": { 13856 "name": "ChIPQC", 13857 "version": "1.44.0", 13858 "sha256": "1zmxyh9a26niix1rch1xl8imc4fwzjbdbbfbcq14hqhdjha0g95p", 13859 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "DiffBind", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "TxDb_Celegans_UCSC_ce6_ensGene", "TxDb_Dmelanogaster_UCSC_dm3_ensGene", "TxDb_Hsapiens_UCSC_hg18_knownGene", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "TxDb_Mmusculus_UCSC_mm9_knownGene", "TxDb_Rnorvegicus_UCSC_rn4_ensGene", "chipseq", "ggplot2", "gtools", "reshape2"], 13860 "broken": true 13861 }, 13862 "Clonality": { 13863 "name": "Clonality", 13864 "version": "1.18.0", 13865 "sha256": "0rx3k8c55q831dhfh5dpkl3px8jj6glx6i3la80r9krx68mbp947", 13866 "depends": ["DNAcopy"], 13867 "broken": true 13868 }, 13869 "CoRegNet": { 13870 "name": "CoRegNet", 13871 "version": "1.6.0", 13872 "sha256": "0ynizawrygpka2isldbfmnlz1zqczx2fv1kbvz1lbm9qwbpj7rn4", 13873 "depends": ["arules", "igraph", "shiny"], 13874 "broken": true 13875 }, 13876 "CoSIA": { 13877 "name": "CoSIA", 13878 "version": "1.8.0", 13879 "sha256": "1xkh2nms6pynpaaw1ckkp2d5vgi93m27jxac9js02cxixg1qmc3l", 13880 "depends": ["AnnotationDbi", "ExperimentHub", "RColorBrewer", "annotationTools", "biomaRt", "dplyr", "ggplot2", "homologene", "magrittr", "org_Ce_eg_db", "org_Dm_eg_db", "org_Dr_eg_db", "org_Hs_eg_db", "org_Mm_eg_db", "org_Rn_eg_db", "plotly", "readr", "stringr", "tibble", "tidyr", "tidyselect"], 13881 "broken": true 13882 }, 13883 "CompGO": { 13884 "name": "CompGO", 13885 "version": "1.6.0", 13886 "sha256": "0n84z3mhg6zb3yafz0803g6cggzpbw31fn933q9bg7pybij0nf1p", 13887 "depends": ["GenomicFeatures", "RDAVIDWebService", "Rgraphviz", "TxDb_Mmusculus_UCSC_mm9_knownGene", "ggplot2", "pathview", "pcaMethods", "reshape2", "rtracklayer"], 13888 "broken": true 13889 }, 13890 "CopyNumber450k": { 13891 "name": "CopyNumber450k", 13892 "version": "1.6.0", 13893 "sha256": "0z4v6x140gzaxf06a73d2qd6dp8gvq62l8xb7bii21r7n089m14i", 13894 "depends": ["Biobase", "BiocGenerics", "DNAcopy", "minfi", "preprocessCore"], 13895 "broken": true 13896 }, 13897 "CopywriteR": { 13898 "name": "CopywriteR", 13899 "version": "2.2.0", 13900 "sha256": "0hmww433hyg4wgi2hx49mwrd4y65myyi00akys3mhdsxn3s0al13", 13901 "depends": ["BiocParallel", "CopyhelpeR", "DNAcopy", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "chipseq", "data_table", "futile_logger", "gtools", "matrixStats"], 13902 "broken": true 13903 }, 13904 "CorMut": { 13905 "name": "CorMut", 13906 "version": "1.12.0", 13907 "sha256": "0ldqw4g15i4r1nv74msn97c75wcr1nvwk1ffnkafvnc8bwcfzfmy", 13908 "depends": ["igraph", "seqinr"], 13909 "broken": true 13910 }, 13911 "CountClust": { 13912 "name": "CountClust", 13913 "version": "1.21.0", 13914 "sha256": "17px9jkpjwz0j2f5h8xv52wh24ilqvlb6dvczjc36lb7mq4cw3sq", 13915 "depends": ["cowplot", "flexmix", "ggplot2", "gtools", "limma", "maptpx", "picante", "plyr", "reshape2", "slam", "SQUAREM"], 13916 "broken": true 13917 }, 13918 "CytoTree": { 13919 "name": "CytoTree", 13920 "version": "1.6.0", 13921 "sha256": "1dsdhwjkd3ngnw50fs6vz048afk47r95vhi0wqj8sip11nhndkd8", 13922 "depends": ["Biobase", "BiocNeighbors", "cluster", "destiny", "flowCore", "FlowSOM", "flowUtils", "ggplot2", "gmodels", "igraph", "limma", "Matrix", "matrixStats", "mclust", "pheatmap", "prettydoc", "RANN", "Rcpp", "Rtsne", "scatterpie", "scatterplot3d", "stringr", "sva", "umap"], 13923 "broken": true 13924 }, 13925 "DASiR": { 13926 "name": "DASiR", 13927 "version": "1.10.0", 13928 "sha256": "1by2655qvskzynvbh47vydm6nl2cmnfqqs25453k29n672a6yyw4", 13929 "depends": ["Biostrings", "GenomicRanges", "IRanges", "XML"], 13930 "broken": true 13931 }, 13932 "DAVIDQuery": { 13933 "name": "DAVIDQuery", 13934 "version": "1.29.0", 13935 "sha256": "0gvm6qjx8y61nbnbz66md74pfc4awj4900pjr8q1m5sip5yzbxj2", 13936 "depends": ["RCurl"], 13937 "broken": true 13938 }, 13939 "DBChIP": { 13940 "name": "DBChIP", 13941 "version": "1.14.0", 13942 "sha256": "1x876cv2j0bdb7jflm663bp7xk32rsxpf9jwwskbl8r4r1ffsapa", 13943 "depends": ["DESeq", "edgeR"], 13944 "broken": true 13945 }, 13946 "DChIPRep": { 13947 "name": "DChIPRep", 13948 "version": "1.0.4", 13949 "sha256": "0cwggkpbza25r2yssyhs9zkwzncmxkd406k2sn2y0rq1kdi08hj2", 13950 "depends": ["DESeq2", "GenomicRanges", "S4Vectors", "assertthat", "fdrtool", "ggplot2", "plyr", "reshape2", "smoothmest", "tidyr"], 13951 "broken": true 13952 }, 13953 "DEComplexDisease": { 13954 "name": "DEComplexDisease", 13955 "version": "1.18.0", 13956 "sha256": "12gw9b0gdwyih51j2gzay6vxhycgc52n8svd0slv6wsbw5rc19lh", 13957 "depends": ["BiocParallel", "ComplexHeatmap", "DESeq2", "edgeR", "Rcpp", "SummarizedExperiment"], 13958 "broken": true 13959 }, 13960 "DEDS": { 13961 "name": "DEDS", 13962 "version": "1.44.0", 13963 "sha256": "079c3in183ybp0c46hqh99grqmbshsnrcax3qz08z5xbc394azna", 13964 "depends": [], 13965 "broken": true 13966 }, 13967 "DELocal": { 13968 "name": "DELocal", 13969 "version": "1.8.0", 13970 "sha256": "0hinzs1220hs7qfjv5na9cn7929wbrnvr409ay0vgphzkh92w30z", 13971 "depends": ["DESeq2", "SummarizedExperiment", "dplyr", "ggplot2", "limma", "matrixStats", "reshape2"], 13972 "broken": true 13973 }, 13974 "DESeq": { 13975 "name": "DESeq", 13976 "version": "1.22.1", 13977 "sha256": "14rc1zcn4a7hkm43ca9js5ffhcm3awjrpl5bx66fj3szibjnnzcb", 13978 "depends": ["Biobase", "BiocGenerics", "MASS", "RColorBrewer", "genefilter", "geneplotter", "lattice", "locfit"], 13979 "broken": true 13980 }, 13981 "DIAlignR": { 13982 "name": "DIAlignR", 13983 "version": "2.12.0", 13984 "sha256": "19zgjnd9sjxx09pcf50fl3w4fmd1gj8g765x114l0cqcpk9qfmm5", 13985 "depends": ["DBI", "RMSNumpress", "RSQLite", "Rcpp", "RcppEigen", "ape", "bit64", "data_table", "dplyr", "ggplot2", "magrittr", "mzR", "phangorn", "pracma", "reticulate", "rlang", "signal", "tidyr", "zoo"], 13986 "broken": true 13987 }, 13988 "DMRforPairs": { 13989 "name": "DMRforPairs", 13990 "version": "1.6.0", 13991 "sha256": "0b5mkhb5gkvfccvpgvklb3ksnq9gv6napcvxzcrph46nmm11i8zc", 13992 "depends": ["GenomicRanges", "Gviz", "R2HTML"], 13993 "broken": true 13994 }, 13995 "DOQTL": { 13996 "name": "DOQTL", 13997 "version": "1.6.0", 13998 "sha256": "0sl7a1hhszrfxn52iw7cz6sl38y7mwk4giw3a7kqj22f1p6bhc6y", 13999 "depends": ["BSgenome_Mmusculus_UCSC_mm10", "Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "QTLRel", "RUnit", "Rsamtools", "VariantAnnotation", "XML", "annotate", "annotationTools", "biomaRt", "corpcor", "doParallel", "foreach", "fpc", "hwriter", "iterators", "mclust", "regress", "rhdf5"], 14000 "broken": true 14001 }, 14002 "DeProViR": { 14003 "name": "DeProViR", 14004 "version": "1.0.0", 14005 "sha256": "0m1nhzq5kl6jyi3d8fzb77iplzc4p85v7lj5q7i7125kjv6bycsm", 14006 "depends": ["BiocFileCache", "PRROC", "caret", "data_table", "dplyr", "fmsb", "ggplot2", "keras", "pROC", "readr"], 14007 "broken": true 14008 }, 14009 "DeconRNASeq": { 14010 "name": "DeconRNASeq", 14011 "version": "1.50.0", 14012 "sha256": "06dkxdikfgiay72z9p0kmk8bayvdbrg641cl39nwk109dms0vc6f", 14013 "depends": ["ggplot2", "limSolve", "pcaMethods"], 14014 "broken": true 14015 }, 14016 "DeepBlueR": { 14017 "name": "DeepBlueR", 14018 "version": "1.27.0", 14019 "sha256": "03v1ag250zq8wj3fxnsg2ii8l93vq6dg9dxqyiqdjnbvxc0y26xg", 14020 "depends": ["data_table", "diffr", "dplyr", "filehash", "foreach", "GenomeInfoDb", "GenomicRanges", "R_utils", "RCurl", "rjson", "rtracklayer", "settings", "stringr", "withr", "XML"], 14021 "broken": true 14022 }, 14023 "Director": { 14024 "name": "Director", 14025 "version": "1.34.0", 14026 "sha256": "0xvpr1j36q46dlfympsivv5kxxnhskywc4fhxk0010yvx92ngpsw", 14027 "depends": ["htmltools"], 14028 "broken": true 14029 }, 14030 "DupChecker": { 14031 "name": "DupChecker", 14032 "version": "1.8.0", 14033 "sha256": "0p75kq178mls765q2v22bj7a727hb1v5rj4wkcagxavcls92vg0p", 14034 "depends": ["RCurl", "R_utils"], 14035 "broken": true 14036 }, 14037 "EBSeqHMM": { 14038 "name": "EBSeqHMM", 14039 "version": "1.4.0", 14040 "sha256": "02ba8famhbp4nxkg8jkwzs63qkfi7hi03h6w1igl2xn2343fnla3", 14041 "depends": ["EBSeq"], 14042 "broken": true 14043 }, 14044 "EDDA": { 14045 "name": "EDDA", 14046 "version": "1.8.0", 14047 "sha256": "0gqgq57a11k7iygjyf3bszx8gm90a8frabmzib7kk84k3wrvynqg", 14048 "depends": ["DESeq", "ROCR", "Rcpp", "baySeq", "edgeR", "snow"], 14049 "broken": true 14050 }, 14051 "ELBOW": { 14052 "name": "ELBOW", 14053 "version": "1.6.0", 14054 "sha256": "1kpprsv1s08qks10raqdh82c9w8dg0saxa1ahhnk1a2whzxj0n3m", 14055 "depends": [], 14056 "broken": true 14057 }, 14058 "ENCODExplorer": { 14059 "name": "ENCODExplorer", 14060 "version": "1.2.4", 14061 "sha256": "0vx4q628g0h1wdcp4hibs44h8avnyin0ccxijrdk94s5n2f91pc2", 14062 "depends": ["RSQLite", "jsonlite"], 14063 "broken": true 14064 }, 14065 "ENVISIONQuery": { 14066 "name": "ENVISIONQuery", 14067 "version": "1.18.0", 14068 "sha256": "1fyp6qyvw5cbapnpjx1s86pss2xhv98s4lqxfxwrsng6p1jh5z89", 14069 "depends": ["XML", "rJava"], 14070 "broken": true 14071 }, 14072 "EasyqpcR": { 14073 "name": "EasyqpcR", 14074 "version": "1.12.0", 14075 "sha256": "0s0ir8bpj3fwg79mzqz57c0crkqqq7hywiwyihcz2cykhsm1r11g", 14076 "depends": ["matrixStats", "plotrix", "plyr"], 14077 "broken": true 14078 }, 14079 "EnhancedVolcano": { 14080 "name": "EnhancedVolcano", 14081 "version": "1.26.0", 14082 "sha256": "19dxqk5dk9443a3949y3b2dhcphhn2lvi6fvlakqxll2lvhjqivi", 14083 "depends": ["ggplot2", "ggrepel"], 14084 "broken": true 14085 }, 14086 "ExpressionView": { 14087 "name": "ExpressionView", 14088 "version": "1.22.0", 14089 "sha256": "1gwhz8q5kyi01jwlwpd39dp292pc6k4v1w0al4653151qb5m55ja", 14090 "depends": ["AnnotationDbi", "GO_db", "KEGG_db", "bitops", "caTools", "eisa", "isa2"], 14091 "broken": true 14092 }, 14093 "FCBF": { 14094 "name": "FCBF", 14095 "version": "2.8.0", 14096 "sha256": "1clg3s2av70j0pm0yj0ckvlklkkg5zb0r057pz6wmklllfkmx1dv", 14097 "depends": ["ggplot2", "gridExtra", "mclust", "pbapply", "SummarizedExperiment"], 14098 "broken": true 14099 }, 14100 "FEM": { 14101 "name": "FEM", 14102 "version": "2.6.0", 14103 "sha256": "1pwbn2igwrd50wn8402f3zwd22h4c8anjmbrls2i6h86ardl046f", 14104 "depends": ["AnnotationDbi", "BiocGenerics", "Matrix", "corrplot", "graph", "igraph", "impute", "limma", "marray", "org_Hs_eg_db"], 14105 "broken": true 14106 }, 14107 "FScanR": { 14108 "name": "FScanR", 14109 "version": "1.10.0", 14110 "sha256": "1v4iq2wlvxf0wbs2d9ip3pcfx3a533pqp4as9pr0f6q57cvqi2bs", 14111 "depends": [], 14112 "broken": true 14113 }, 14114 "FindMyFriends": { 14115 "name": "FindMyFriends", 14116 "version": "1.0.7", 14117 "sha256": "0ga0iwscbcczysldizgp8g19gsyszfw4vgbgs45q9px95603z0cg", 14118 "depends": ["Biobase", "BiocParallel", "Biostrings", "IRanges", "Matrix", "Rcpp", "S4Vectors", "digest", "dplyr", "filehash", "ggdendro", "ggplot2", "gtable", "igraph", "kebabs", "reshape2"], 14119 "broken": true 14120 }, 14121 "FlowRepositoryR": { 14122 "name": "FlowRepositoryR", 14123 "version": "1.2.0", 14124 "sha256": "1y1y7g9111z55cwi2ph44yqib41234g77xwsybk6irlq1anizz7p", 14125 "depends": ["RCurl", "XML"], 14126 "broken": true 14127 }, 14128 "FoldGO": { 14129 "name": "FoldGO", 14130 "version": "1.18.0", 14131 "sha256": "0h08yv1kykllaanc562ncwv3ajic7cd4wcqba24nlbh6agsazwyk", 14132 "depends": ["ggplot2", "tidyr", "topGO"], 14133 "broken": true 14134 }, 14135 "FourCSeq": { 14136 "name": "FourCSeq", 14137 "version": "1.4.0", 14138 "sha256": "1xh0l90hp6jy9j0xkh78dm9kyk90zzlg04yfrzd4v12mwljs8r19", 14139 "depends": ["Biobase", "Biostrings", "DESeq2", "GenomicAlignments", "GenomicRanges", "LSD", "Matrix", "Rsamtools", "SummarizedExperiment", "fda", "ggbio", "ggplot2", "gtools", "reshape2", "rtracklayer"], 14140 "broken": true 14141 }, 14142 "FunChIP": { 14143 "name": "FunChIP", 14144 "version": "1.28.0", 14145 "sha256": "1qhwabm7vgjqmgxdla6qs70sncvzjc8qh5vpq5xqp50hk1lli7f1", 14146 "depends": ["doParallel", "fda", "foreach", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "RColorBrewer", "Rcpp", "Rsamtools", "shiny"], 14147 "broken": true 14148 }, 14149 "FunciSNP": { 14150 "name": "FunciSNP", 14151 "version": "1.12.0", 14152 "sha256": "1125ismkp2sprshv4b39l6bycdlry3933jaliva17c0bgjr27jhm", 14153 "depends": ["AnnotationDbi", "ChIPpeakAnno", "FunciSNP_data", "GenomicRanges", "IRanges", "Rsamtools", "TxDb_Hsapiens_UCSC_hg19_knownGene", "VariantAnnotation", "ggplot2", "org_Hs_eg_db", "plyr", "reshape", "rtracklayer", "scales", "snpStats"], 14154 "broken": true 14155 }, 14156 "GAPGOM": { 14157 "name": "GAPGOM", 14158 "version": "1.11.0", 14159 "sha256": "0sl97w5zx4zdrdbcwayqyvgxspaxpbils3mpsrim0zlspjrjcy6z", 14160 "depends": ["AnnotationDbi", "Biobase", "BiocFileCache", "data_table", "dplyr", "fastmatch", "GEOquery", "GO_db", "GOSemSim", "graph", "igraph", "magrittr", "Matrix", "matrixStats", "org_Hs_eg_db", "org_Mm_eg_db", "plyr", "RBGL"], 14161 "broken": true 14162 }, 14163 "GCSConnection": { 14164 "name": "GCSConnection", 14165 "version": "1.7.0", 14166 "sha256": "1psmw3825whyzvbzqpqksgcl09b6kfyb8k5vny6ljkjbac1jzvnf", 14167 "depends": ["googleAuthR", "googleCloudStorageR", "httr", "jsonlite", "Rcpp"], 14168 "broken": true 14169 }, 14170 "GCSFilesystem": { 14171 "name": "GCSFilesystem", 14172 "version": "1.6.0", 14173 "sha256": "0qk8xyg06f71y4r1q1zpcj89irh9i6cd9z6nqlx635x8if84sh6d", 14174 "depends": [], 14175 "broken": true 14176 }, 14177 "GCSscore": { 14178 "name": "GCSscore", 14179 "version": "1.14.0", 14180 "sha256": "0fqr0sgplpbkdpvwgi8fpmwmnqja41622pvkkzsalbzai021hgp3", 14181 "depends": ["affxparser", "Biobase", "BiocManager", "data_table", "devtools", "dplR", "RSQLite", "stringr"], 14182 "broken": true 14183 }, 14184 "GENE_E": { 14185 "name": "GENE.E", 14186 "version": "1.10.0", 14187 "sha256": "1czm1j144i842d7lf01c9gmyifikp4a66sq49i7rgpzbiz3pndkf", 14188 "depends": ["RCurl", "rhdf5"], 14189 "broken": true 14190 }, 14191 "GEOexplorer": { 14192 "name": "GEOexplorer", 14193 "version": "1.14.0", 14194 "sha256": "144pj7aj93rjg315biizapg1m9yywyfx27pk9646klqnrnp2yxi5", 14195 "depends": ["Biobase", "DT", "GEOquery", "R_utils", "XML", "car", "edgeR", "enrichR", "factoextra", "ggplot2", "heatmaply", "htmltools", "httr", "impute", "knitr", "limma", "markdown", "pheatmap", "plotly", "readxl", "scales", "shiny", "shinyHeatmaply", "shinybusy", "shinycssloaders", "stringr", "sva", "umap", "xfun", "xml2"], 14196 "broken": true 14197 }, 14198 "GEOsearch": { 14199 "name": "GEOsearch", 14200 "version": "1.0.1", 14201 "sha256": "1zag3rg2cfs0zfh092rzwhshnkncrv2p88flz9hy2n350k1xnyc4", 14202 "depends": ["org_Hs_eg_db", "org_Mm_eg_db"], 14203 "broken": true 14204 }, 14205 "GGBase": { 14206 "name": "GGBase", 14207 "version": "3.32.0", 14208 "sha256": "15vvwigv9xy87dl2c795c3abpnrzr364m4sbslmns403rg8dpsiw", 14209 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "Matrix", "S4Vectors", "SummarizedExperiment", "digest", "genefilter", "limma", "snpStats"], 14210 "broken": true 14211 }, 14212 "GGtools": { 14213 "name": "GGtools", 14214 "version": "5.6.0", 14215 "sha256": "1ndvlyfzjn519z9zh6kf5sdjaz3ckracgyf2lxp23nchm2311lf0", 14216 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "Biostrings", "GGBase", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "ROCR", "Rsamtools", "S4Vectors", "VariantAnnotation", "biglm", "bit", "data_table", "ff", "ggplot2", "hexbin", "iterators", "reshape2", "rtracklayer", "snpStats"], 14217 "broken": true 14218 }, 14219 "GISPA": { 14220 "name": "GISPA", 14221 "version": "1.26.0", 14222 "sha256": "19vbcfdf959xs6kgds37ij3qay9x61dzrlvcs238m7hywl4dn3lz", 14223 "depends": ["Biobase", "changepoint", "data_table", "genefilter", "GSEABase", "HH", "lattice", "latticeExtra", "plyr", "scatterplot3d"], 14224 "broken": true 14225 }, 14226 "GOFunction": { 14227 "name": "GOFunction", 14228 "version": "1.18.0", 14229 "sha256": "00pdxf24sxdnh31h69c5zjhl1j2jv1ag91ay3a9w62p07bcg82l6", 14230 "depends": ["AnnotationDbi", "Biobase", "GO_db", "Rgraphviz", "SparseM", "graph"], 14231 "broken": true 14232 }, 14233 "GOSim": { 14234 "name": "GOSim", 14235 "version": "1.8.0", 14236 "sha256": "14dyazr7p9p7h1cckbmd5yjj76718lqgfnqbcrrz52qyk0dqz6wx", 14237 "depends": ["AnnotationDbi", "GO_db", "Matrix", "RBGL", "Rcpp", "annotate", "cluster", "corpcor", "flexmix", "graph", "org_Hs_eg_db", "topGO"], 14238 "broken": true 14239 }, 14240 "GOsummaries": { 14241 "name": "GOsummaries", 14242 "version": "2.4.7", 14243 "sha256": "0kl77jqd2bdbp8v2rrjp21j265r05fnagpz8jwj8m9scgrd5hwh4", 14244 "depends": ["Rcpp", "gProfileR", "ggplot2", "gtable", "limma", "plyr", "reshape2"], 14245 "broken": true 14246 }, 14247 "GRridge": { 14248 "name": "GRridge", 14249 "version": "1.22.0", 14250 "sha256": "0vmwm50dwk3im3qx40vh9ipmfqywzz5fmmm79b74zjcd3qjrznf3", 14251 "depends": ["glmnet", "graph", "Iso", "mvtnorm", "penalized", "survival"], 14252 "broken": true 14253 }, 14254 "GeDi": { 14255 "name": "GeDi", 14256 "version": "1.4.0", 14257 "sha256": "0mxnbk0xqwc8v4vn50s59gb8gxl5y4dwy8n6sg2ydd23qzd2al9p", 14258 "depends": ["BiocFileCache", "BiocNeighbors", "BiocParallel", "ComplexHeatmap", "DT", "GOSemSim", "GeneTonic", "Matrix", "RColorBrewer", "STRINGdb", "bs4Dash", "circlize", "cluster", "dplyr", "fontawesome", "ggdendro", "ggplot2", "igraph", "plotly", "readxl", "rintrojs", "scales", "shiny", "shinyBS", "shinyWidgets", "shinycssloaders", "tm", "visNetwork", "wordcloud2"], 14259 "broken": true 14260 }, 14261 "GenVisR": { 14262 "name": "GenVisR", 14263 "version": "1.39.0", 14264 "sha256": "1ax1r53zdjgmgfkj6y9hfd6w19wprpsm6mfbpi168cdskivnpva3", 14265 "depends": ["AnnotationDbi", "BSgenome", "BiocGenerics", "Biostrings", "DBI", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "VariantAnnotation", "biomaRt", "data_table", "ggplot2", "gridExtra", "gtable", "gtools", "plyr", "reshape2", "scales", "viridis"], 14266 "broken": true 14267 }, 14268 "GeneAccord": { 14269 "name": "GeneAccord", 14270 "version": "1.15.0", 14271 "sha256": "1dlnqdcrl1fv5yf0zwfgkqfd2x19fv6q84p7c730nmnnaqal6md1", 14272 "depends": ["biomaRt", "caTools", "dplyr", "ggplot2", "ggpubr", "gtools", "magrittr", "maxLik", "RColorBrewer", "reshape2", "tibble"], 14273 "broken": true 14274 }, 14275 "GeneAnswers": { 14276 "name": "GeneAnswers", 14277 "version": "2.12.0", 14278 "sha256": "1gacvc1vd0sl6jn0r14w4n37hsrmx6m5k1l7d2a5m3qssyk6l6n3", 14279 "depends": ["Biobase", "Heatplus", "MASS", "RBGL", "RColorBrewer", "RCurl", "RSQLite", "XML", "annotate", "downloader", "igraph"], 14280 "broken": true 14281 }, 14282 "GeneGeneInteR": { 14283 "name": "GeneGeneInteR", 14284 "version": "1.33.0", 14285 "sha256": "1wsm0l14mx2qd9gcs6m2n2pn0sgymf79fm8kvxjxvijqjv8n82ca", 14286 "depends": ["FactoMineR", "GenomicRanges", "IRanges", "Rsamtools", "data_table", "igraph", "kernlab", "mvtnorm", "snpStats"], 14287 "broken": true 14288 }, 14289 "GeneSelector": { 14290 "name": "GeneSelector", 14291 "version": "2.20.0", 14292 "sha256": "179mjqk9w4zm33mhja7hmwphpnxsv32mh60avs2mqmq9fi9z6pdh", 14293 "depends": ["Biobase", "limma", "multtest", "samr", "siggenes"], 14294 "broken": true 14295 }, 14296 "GeneTonic": { 14297 "name": "GeneTonic", 14298 "version": "3.2.0", 14299 "sha256": "1q61akm9sllrjbk3dy2mbvcv0fl10qyqvgvwaz1klixkfwi03hm3", 14300 "depends": ["AnnotationDbi", "ComplexHeatmap", "ComplexUpset", "DESeq2", "DT", "GO_db", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "backbone", "bs4Dash", "circlize", "colorspace", "colourpicker", "dendextend", "dplyr", "dynamicTreeCut", "expm", "ggforce", "ggplot2", "ggrepel", "ggridges", "igraph", "matrixStats", "mosdef", "plotly", "rintrojs", "rlang", "rmarkdown", "scales", "shiny", "shinyAce", "shinyWidgets", "shinycssloaders", "tidyr", "tippy", "viridis", "visNetwork"], 14301 "broken": true 14302 }, 14303 "GeneticsDesign": { 14304 "name": "GeneticsDesign", 14305 "version": "1.38.0", 14306 "sha256": "1yh8s40fr0yqbch7ix9y4p22ih0008xpjy5nn5x37y575l41hhwh", 14307 "depends": ["gmodels", "gtools", "mvtnorm"], 14308 "broken": true 14309 }, 14310 "GenoGAM": { 14311 "name": "GenoGAM", 14312 "version": "2.11.0", 14313 "sha256": "058qix2h0zm2k9csmbdhci2wqih3lyggjj591cqn0ls2nv7bnyvj", 14314 "depends": ["BiocParallel", "Biostrings", "data_table", "DelayedArray", "DESeq2", "futile_logger", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "HDF5Array", "IRanges", "Matrix", "Rcpp", "RcppArmadillo", "rhdf5", "Rsamtools", "S4Vectors", "sparseinv", "SummarizedExperiment"], 14315 "broken": true 14316 }, 14317 "GenoView": { 14318 "name": "GenoView", 14319 "version": "1.3.0", 14320 "sha256": "09k9xjmx3qmsfr3a4vrfgs73r0xsymf5m4gl0zjjk4cnfk7bs41v", 14321 "depends": ["GenomicRanges", "biovizBase", "ggbio", "ggplot2", "gridExtra"], 14322 "broken": true 14323 }, 14324 "GenomeGraphs": { 14325 "name": "GenomeGraphs", 14326 "version": "1.30.0", 14327 "sha256": "1wkjcg6w95wlrdgaskc3xndl0azmxhxnsipf9qrj057gf2rpx7zf", 14328 "depends": ["biomaRt"], 14329 "broken": true 14330 }, 14331 "Genominator": { 14332 "name": "Genominator", 14333 "version": "1.24.0", 14334 "sha256": "1rqzxbji5wh6dshjsprj1mzps08l07gxmjir9naj6lsj2q0xhn9p", 14335 "depends": ["BiocGenerics", "DBI", "GenomeGraphs", "IRanges", "RSQLite"], 14336 "broken": true 14337 }, 14338 "GoogleGenomics": { 14339 "name": "GoogleGenomics", 14340 "version": "1.2.0", 14341 "sha256": "1z87jmd5vzg5v93bv9k3998wqhnk5p2v9d2qr9g0xxjvxw2q78fm", 14342 "depends": ["Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "VariantAnnotation", "httr", "rjson"], 14343 "broken": true 14344 }, 14345 "GraphPAC": { 14346 "name": "GraphPAC", 14347 "version": "1.12.1", 14348 "sha256": "1fa64jam3cl1khv8jspwjb9myifmgx0kwg0b601bia578bjcdj7d", 14349 "depends": ["RMallow", "TSP", "iPAC", "igraph"], 14350 "broken": true 14351 }, 14352 "HCsnip": { 14353 "name": "HCsnip", 14354 "version": "1.10.0", 14355 "sha256": "0x4lpx13bhr2w5yhrcsc89g0x4q1dy0j588h210ziizgh67qqcrs", 14356 "depends": ["Biobase", "clusterRepro", "coin", "fpc", "impute", "randomForestSRC", "sigaR", "sm", "survival"], 14357 "broken": true 14358 }, 14359 "HPAStainR": { 14360 "name": "HPAStainR", 14361 "version": "1.9.0", 14362 "sha256": "1bjysi3x8248f262v4rzi2y50rlzryb987wbvdjy6af84nq7hd09", 14363 "depends": ["data_table", "dplyr", "scales", "shiny", "stringr", "tibble", "tidyr"], 14364 "broken": true 14365 }, 14366 "HPiP": { 14367 "name": "HPiP", 14368 "version": "1.14.0", 14369 "sha256": "0dbpzacyhwv0080ql3p3gsrmclb5sil9rj3kh2lf7b61qsikh701", 14370 "depends": ["MCL", "PRROC", "caret", "corrplot", "dplyr", "ggplot2", "httr", "igraph", "magrittr", "pROC", "protr", "purrr", "readr", "stringr", "tibble", "tidyr"], 14371 "broken": true 14372 }, 14373 "HTSanalyzeR": { 14374 "name": "HTSanalyzeR", 14375 "version": "2.22.0", 14376 "sha256": "01mb273v1i9k0d2gbl9mpmr4rrnx49s3srv0yh1znvmwx0hmfyq2", 14377 "depends": ["AnnotationDbi", "BioNet", "GSEABase", "RankProd", "biomaRt", "cellHTS2", "graph", "igraph"], 14378 "broken": true 14379 }, 14380 "HTSeqGenie": { 14381 "name": "HTSeqGenie", 14382 "version": "3.20.1", 14383 "sha256": "0bg86jiv45899gw9x4hhvqf525vfwkzj2b5jk7026cq5vmjc0k5j", 14384 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "Cairo", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "VariantAnnotation", "VariantTools", "chipseq", "gmapR", "hwriter", "rtracklayer"], 14385 "broken": true 14386 }, 14387 "Harshlight": { 14388 "name": "Harshlight", 14389 "version": "1.79.0", 14390 "sha256": "1jm0ia06ls1m7dsbzp1hk68qi5wbqzhcf6x66534bj1kxdll17k7", 14391 "depends": ["Biobase", "affy", "altcdfenvs"], 14392 "broken": true 14393 }, 14394 "HiCool": { 14395 "name": "HiCool", 14396 "version": "1.8.0", 14397 "sha256": "0cnzbi4if3cn0lr78yh4a76kn3pv8c332w69s3l9gsqxvjx16kqs", 14398 "depends": ["BiocIO", "GenomicRanges", "HiCExperiment", "IRanges", "InteractionSet", "S4Vectors", "basilisk", "dplyr", "plotly", "reticulate", "rmarkdown", "rmdformats", "sessioninfo", "stringr", "vroom"], 14399 "broken": true 14400 }, 14401 "HumanTranscriptomeCompendium": { 14402 "name": "HumanTranscriptomeCompendium", 14403 "version": "1.20.0", 14404 "sha256": "1y46zsl08k6sdih8psar85fyc5dfk2vraxmfry70zx57vbjbin92", 14405 "depends": ["BiocManager", "S4Vectors", "SummarizedExperiment", "shiny", "ssrch"], 14406 "broken": true 14407 }, 14408 "IMAS": { 14409 "name": "IMAS", 14410 "version": "1.32.0", 14411 "sha256": "1b1vy4mdnna15ckmh6n5jqz4bkyq4izm5zij71brg3b21214c0ja", 14412 "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "IVAS", "Matrix", "Rsamtools", "S4Vectors", "doParallel", "foreach", "ggfortify", "ggplot2", "gridExtra", "lattice", "lme4", "survival"], 14413 "broken": true 14414 }, 14415 "IPPD": { 14416 "name": "IPPD", 14417 "version": "1.18.0", 14418 "sha256": "1kl4rx6rdmpkm7bd2w8ncvz4sb8x6wljvxkif2l17yflsp1wjvp2", 14419 "depends": ["MASS", "Matrix", "XML", "bitops", "digest"], 14420 "broken": true 14421 }, 14422 "IRISFGM": { 14423 "name": "IRISFGM", 14424 "version": "1.8.0", 14425 "sha256": "1n13rsbg5y0xnr6in18silifx8jhqzjj1vb5kpjgy5ml55im1s5r", 14426 "depends": ["AdaptGauss", "AnnotationDbi", "anocva", "clusterProfiler", "colorspace", "DEsingle", "DrImpute", "ggplot2", "ggpubr", "ggraph", "igraph", "knitr", "Matrix", "MCL", "mixtools", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "Polychrome", "RColorBrewer", "Rcpp", "scater", "scran", "Seurat", "SingleCellExperiment"], 14427 "broken": true 14428 }, 14429 "IdMappingAnalysis": { 14430 "name": "IdMappingAnalysis", 14431 "version": "1.14.0", 14432 "sha256": "11rn1b6665b64h3a4mb8qkg5kp5l9ha6aa14f512k7lzs1vcczpm", 14433 "depends": ["Biobase", "RColorBrewer", "R_oo", "boot", "mclust", "rChoiceDialogs"], 14434 "broken": true 14435 }, 14436 "IdMappingRetrieval": { 14437 "name": "IdMappingRetrieval", 14438 "version": "1.18.2", 14439 "sha256": "0wl2ybv23z84rlq2szk46kvcdm0bmqy0mjga9n33wz1c04br2bxj", 14440 "depends": ["AffyCompatible", "ENVISIONQuery", "RCurl", "R_methodsS3", "R_oo", "XML", "biomaRt", "rChoiceDialogs"], 14441 "broken": true 14442 }, 14443 "Imetagene": { 14444 "name": "Imetagene", 14445 "version": "1.0.0", 14446 "sha256": "1di9nx5ad0wd17byn740azx9yb6hd12dzvlfl8s5iyas4z9qzwya", 14447 "depends": ["ggplot2", "metagene", "shiny", "shinyBS", "shinyFiles", "shinythemes"], 14448 "broken": true 14449 }, 14450 "ImmuneSpaceR": { 14451 "name": "ImmuneSpaceR", 14452 "version": "1.30.0", 14453 "sha256": "0lhilrh4xyw1cvqnx4b6g0llm9b1i4l2r476d4hmypkkgl25q8n7", 14454 "depends": ["Biobase", "curl", "data_table", "digest", "flowCore", "flowWorkspace", "ggplot2", "gplots", "heatmaply", "httr", "jsonlite", "pheatmap", "plotly", "preprocessCore", "R6", "Rlabkey", "rmarkdown", "scales"], 14455 "broken": true 14456 }, 14457 "IntOMICS": { 14458 "name": "IntOMICS", 14459 "version": "1.2.0", 14460 "sha256": "1qhni8p8zap9szi499jrdxkacdrb7vdd4va5h4n0kdi4qr80vrzh", 14461 "depends": ["bestNormalize", "bnlearn", "bnstruct", "cowplot", "ggplot2", "ggraph", "gplots", "igraph", "matrixStats", "numbers", "RColorBrewer", "rlang", "SummarizedExperiment"], 14462 "broken": true 14463 }, 14464 "InterMineR": { 14465 "name": "InterMineR", 14466 "version": "1.26.0", 14467 "sha256": "0isw4rg89139xmrcfb9r7jc3z8jj1my4radhinah0vad2cwb36l0", 14468 "depends": ["Biostrings", "GenomicRanges", "IRanges", "RCurl", "RJSONIO", "S4Vectors", "SummarizedExperiment", "XML", "httr", "igraph", "sqldf", "xml2"], 14469 "broken": true 14470 }, 14471 "IsoGeneGUI": { 14472 "name": "IsoGeneGUI", 14473 "version": "2.6.0", 14474 "sha256": "1b7my9ri3kwi4rbdymcnwdjzv88pgdfjf2ax4gls0v4460hwg5az", 14475 "depends": ["Biobase", "Iso", "ORCME", "ORIClust", "RColorBrewer", "Rcpp", "ff", "geneplotter", "goric", "jpeg", "multtest", "relimp", "tkrplot", "xlsx"], 14476 "broken": true 14477 }, 14478 "KEGGprofile": { 14479 "name": "KEGGprofile", 14480 "version": "1.12.0", 14481 "sha256": "08yg0vn7d0yyamwj8s9bg9130y1dag34w5j9dhi00x7381jnrxwr", 14482 "depends": ["AnnotationDbi", "KEGGREST", "KEGG_db", "TeachingDemos", "XML", "biomaRt", "png"], 14483 "broken": true 14484 }, 14485 "LMGene": { 14486 "name": "LMGene", 14487 "version": "2.26.0", 14488 "sha256": "0mfs8kpirwkv8salg6aacy0hr0zwmmxr7pzh88sxj3x71k2dclzi", 14489 "depends": ["Biobase", "affy", "multtest", "survival"], 14490 "broken": true 14491 }, 14492 "LPEadj": { 14493 "name": "LPEadj", 14494 "version": "1.30.0", 14495 "sha256": "0ll9n3wkaink16laj2y98hb0kx5dglz776zlwdfkw54l1fjvvj5h", 14496 "depends": ["LPE"], 14497 "broken": true 14498 }, 14499 "LVSmiRNA": { 14500 "name": "LVSmiRNA", 14501 "version": "1.20.0", 14502 "sha256": "1q43harvk7q5wb8yjffhvzs4dxl8h5vp60ngym5vcvapxr8iym3w", 14503 "depends": ["Biobase", "BiocGenerics", "MASS", "SparseM", "affy", "limma", "quantreg", "vsn", "zlibbioc"], 14504 "broken": true 14505 }, 14506 "LinTInd": { 14507 "name": "LinTInd", 14508 "version": "1.12.0", 14509 "sha256": "0hk602dvj93j3nqplm8nrxy51xl59ynplif63w5scbvngnvhlc9y", 14510 "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors", "ape", "cowplot", "data_tree", "dplyr", "ggnewscale", "ggplot2", "ggtree", "networkD3", "pheatmap", "purrr", "pwalign", "reshape2", "rlist", "stringdist", "stringr"], 14511 "broken": true 14512 }, 14513 "LineagePulse": { 14514 "name": "LineagePulse", 14515 "version": "1.21.0", 14516 "sha256": "09x1i7slysqf3dpjzck6rgfzhyswaj0kk8i047yscg8fcaksbmqg", 14517 "depends": ["BiocParallel", "circlize", "ComplexHeatmap", "ggplot2", "gplots", "knitr", "Matrix", "RColorBrewer", "SingleCellExperiment", "SummarizedExperiment"], 14518 "broken": true 14519 }, 14520 "LowMACA": { 14521 "name": "LowMACA", 14522 "version": "1.2.0", 14523 "sha256": "12jm8psg7rnrsxydcqzfgiryy6lk5mxyximfzn7hnqqvxbs3wc55", 14524 "depends": ["BiocParallel", "Biostrings", "LowMACAAnnotation", "RColorBrewer", "data_table", "motifStack", "reshape2", "stringr"], 14525 "broken": true 14526 }, 14527 "M3D": { 14528 "name": "M3D", 14529 "version": "1.4.0", 14530 "sha256": "088ghd9r5jr51179cj9hbk1dpj4f9fkrbgyghlq29w2bbgzc57xx", 14531 "depends": ["BiSeq", "GenomicRanges", "IRanges"], 14532 "broken": true 14533 }, 14534 "MACPET": { 14535 "name": "MACPET", 14536 "version": "1.15.1", 14537 "sha256": "0742i3fxg2793lhgpxb4whh6mwvzd4bn86ykd0rv8sgilxyq5zsl", 14538 "depends": ["BH", "bigmemory", "BiocParallel", "Biostrings", "futile_logger", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "GEOquery", "gtools", "InteractionSet", "intervals", "IRanges", "knitr", "plyr", "Rbowtie", "Rcpp", "Rsamtools", "rtracklayer", "S4Vectors", "ShortRead"], 14539 "broken": true 14540 }, 14541 "MADSEQ": { 14542 "name": "MADSEQ", 14543 "version": "1.34.0", 14544 "sha256": "1fir4xvhg9n33wzq0s5191k9z1ywj02g8khz1337hp137i2vn6jy", 14545 "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "VGAM", "VariantAnnotation", "coda", "preprocessCore", "rjags", "rtracklayer", "vcfR", "zlibbioc"], 14546 "broken": true 14547 }, 14548 "MAGeCKFlute": { 14549 "name": "MAGeCKFlute", 14550 "version": "2.9.0", 14551 "sha256": "1m2yq73q9wwv5kfybgnkdb877dy539x9vpx713pr6xjpkqvksfiv", 14552 "depends": ["Biobase", "DOSE", "clusterProfiler", "depmap", "enrichplot", "ggplot2", "ggrepel", "gridExtra", "msigdbr", "pathview", "reshape2"], 14553 "broken": true 14554 }, 14555 "MCRestimate": { 14556 "name": "MCRestimate", 14557 "version": "2.26.0", 14558 "sha256": "1igfffsgz6m4rl2a5fnkb92r5x4qjr2yl8gaj3ws8478q3aq0bgd", 14559 "depends": ["Biobase", "RColorBrewer", "e1071", "golubEsets", "pamr", "randomForest"], 14560 "broken": true 14561 }, 14562 "MGFR": { 14563 "name": "MGFR", 14564 "version": "1.34.0", 14565 "sha256": "02d2m9yj5yq66b638jrwavpy2fsl41chh3gb13b4k0sca120bbxb", 14566 "depends": ["annotate", "biomaRt"], 14567 "broken": true 14568 }, 14569 "MIGSA": { 14570 "name": "MIGSA", 14571 "version": "1.21.0", 14572 "sha256": "0b7w9lzi8xb1vzh7zahw7wh9jm7x1y04rs2gvvjmfbdfw085rdpm", 14573 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "data_table", "edgeR", "futile_logger", "ggdendro", "ggplot2", "GO_db", "GOstats", "graph", "GSEABase", "ismev", "jsonlite", "limma", "matrixStats", "org_Hs_eg_db", "RBGL", "reshape2", "Rgraphviz", "vegan"], 14574 "broken": true 14575 }, 14576 "MIMOSA": { 14577 "name": "MIMOSA", 14578 "version": "1.8.1", 14579 "sha256": "1mkxp83gwxw581gz13vb8lbl2pff7al75lhjcvwxv6gxb1k272xi", 14580 "depends": ["Biobase", "Formula", "MASS", "MCMCpack", "Rcpp", "RcppArmadillo", "coda", "data_table", "ggplot2", "modeest", "plyr", "pracma", "reshape", "scales", "testthat"], 14581 "broken": true 14582 }, 14583 "MMAPPR2": { 14584 "name": "MMAPPR2", 14585 "version": "1.14.0", 14586 "sha256": "14m41hi79f7m2qigjjcgy08awrf0654ridgm6wxcq8cmmlm68g8a", 14587 "depends": ["Biobase", "BiocGenerics", "BiocParallel", "data_table", "dplyr", "ensemblVEP", "GenomeInfoDb", "GenomicRanges", "gmapR", "IRanges", "magrittr", "Rsamtools", "S4Vectors", "stringr", "tidyr", "VariantAnnotation", "VariantTools"], 14588 "broken": true 14589 }, 14590 "MMDiff": { 14591 "name": "MMDiff", 14592 "version": "1.10.0", 14593 "sha256": "0v000a87ciw83xj6p2443k1zs1w98ax38nzaf643wqmb8szwr6vf", 14594 "depends": ["Biobase", "DiffBind", "GenomicRanges", "IRanges", "Rsamtools"], 14595 "broken": true 14596 }, 14597 "MMUPHin": { 14598 "name": "MMUPHin", 14599 "version": "1.22.0", 14600 "sha256": "0d8i9b6pjwz409jd46fm1n9h21hzg8zgzpvchywpyc1k896fvz4l", 14601 "depends": ["Maaslin2", "cowplot", "dplyr", "fpc", "ggplot2", "igraph", "metafor", "stringr", "tidyr"], 14602 "broken": true 14603 }, 14604 "MQmetrics": { 14605 "name": "MQmetrics", 14606 "version": "1.10.0", 14607 "sha256": "15jkmdj2k5h8vbi332y7b4xzm2330g2s13l6lf2d1v9pg5aqrisq", 14608 "depends": ["cowplot", "dplyr", "ggforce", "gghalves", "ggplot2", "ggpubr", "ggrepel", "gridExtra", "gtable", "knitr", "magrittr", "plyr", "purrr", "RColorBrewer", "readr", "reshape2", "rlang", "rmarkdown", "scales", "stringr", "tidyr"], 14609 "broken": true 14610 }, 14611 "MSEADbi": { 14612 "name": "MSEADbi", 14613 "version": "1.2.0", 14614 "sha256": "1g1kg3nh7iwg5nrpmig6srw6as4yfwmbqn965pffrk0zp19llsbf", 14615 "depends": ["AnnotationDbi", "Biobase", "DBI", "RSQLite"], 14616 "broken": true 14617 }, 14618 "MSGFgui": { 14619 "name": "MSGFgui", 14620 "version": "1.4.0", 14621 "sha256": "0pb9i81pqnz05jrwqh9myz5zchdn8ng5nrsv3cmdg4713yskqpcw", 14622 "depends": ["MSGFplus", "mzID", "mzR", "shiny", "shinyFiles", "xlsx"], 14623 "broken": true 14624 }, 14625 "MSGFplus": { 14626 "name": "MSGFplus", 14627 "version": "1.4.0", 14628 "sha256": "1hw40kyhkxm0iy60n3y1cw2k52q5vjl47k4z5x34syq5d14iplva", 14629 "depends": ["mzID"], 14630 "broken": true 14631 }, 14632 "MSstatsSampleSize": { 14633 "name": "MSstatsSampleSize", 14634 "version": "1.13.0", 14635 "sha256": "09gmlqxb65pa4wxh5bryb6lhs68zrfaqfl7n3k9shvzi3iw02vp3", 14636 "depends": ["BiocParallel", "caret", "ggplot2", "gridExtra", "MSstats", "reshape2"], 14637 "broken": true 14638 }, 14639 "MSstatsTMTPTM": { 14640 "name": "MSstatsTMTPTM", 14641 "version": "1.1.2", 14642 "sha256": "16qnddwhwhjjfr5akdrmp93gkxq2r41s82hb1blbz47lwbj5kaj5", 14643 "depends": ["dplyr", "ggplot2", "gridExtra", "MSstatsTMT", "Rcpp", "reshape2", "stringr"], 14644 "broken": true 14645 }, 14646 "Maaslin2": { 14647 "name": "Maaslin2", 14648 "version": "1.22.0", 14649 "sha256": "10hdjhi1ykk513hzvs0bi6avzghqmkqns8knhz3ycv7bj3ynp70x", 14650 "depends": ["MASS", "biglm", "car", "chemometrics", "cplm", "data_table", "dplyr", "edgeR", "ggplot2", "glmmTMB", "hash", "lme4", "lmerTest", "logging", "metagenomeSeq", "optparse", "pbapply", "pcaPP", "pheatmap", "pscl", "robustbase", "tibble", "vegan"], 14651 "broken": true 14652 }, 14653 "Macarron": { 14654 "name": "Macarron", 14655 "version": "1.12.2", 14656 "sha256": "1gmpw9lf39hdvaqfwqkr3vbq32g5ik8i48njdfmq2f42kdmdpxy6", 14657 "depends": ["BiocParallel", "DelayedArray", "Maaslin2", "RJSONIO", "SummarizedExperiment", "WGCNA", "data_table", "dynamicTreeCut", "ff", "httr", "logging", "plyr", "psych", "xml2"], 14658 "broken": true 14659 }, 14660 "MeSHSim": { 14661 "name": "MeSHSim", 14662 "version": "1.2.0", 14663 "sha256": "1wgc2s1080sm2dn9ny4c1kpbcmbv4gv91h7jmgya9p8lk224aasr", 14664 "depends": ["RCurl", "XML"], 14665 "broken": true 14666 }, 14667 "Melissa": { 14668 "name": "Melissa", 14669 "version": "1.24.0", 14670 "sha256": "0y80p2jp4i7wsgqilaz1xkp573z97zxx0gwc7bg6d78bqsych11b", 14671 "depends": ["BPRMeth", "BiocStyle", "GenomicRanges", "MCMCpack", "ROCR", "assertthat", "cowplot", "data_table", "doParallel", "foreach", "ggplot2", "magrittr", "matrixcalc", "mclust", "mvtnorm", "truncnorm"], 14672 "broken": true 14673 }, 14674 "MergeMaid": { 14675 "name": "MergeMaid", 14676 "version": "2.42.0", 14677 "sha256": "1ajmrcpvzfjk0bkm2v3yklry91w5cxpjhgjr9hfszzldfhh5sfw4", 14678 "depends": ["Biobase", "MASS", "survival"], 14679 "broken": true 14680 }, 14681 "MetMashR": { 14682 "name": "MetMashR", 14683 "version": "1.2.0", 14684 "sha256": "1505j1jvmgnrxpbpkyh6am0baqmy312sc0fkg1dgzimq6pmwm170", 14685 "depends": ["cowplot", "dplyr", "ggplot2", "ggthemes", "httr", "rlang", "scales", "struct"], 14686 "broken": true 14687 }, 14688 "MetaVolcanoR": { 14689 "name": "MetaVolcanoR", 14690 "version": "1.14.0", 14691 "sha256": "11fxjv0kb65wc2237rh3340j72v3zsd4s019bi07rbpqnl246pnj", 14692 "depends": ["cowplot", "data_table", "dplyr", "ggplot2", "htmlwidgets", "metafor", "metap", "plotly", "rlang", "tidyr", "topconfects"], 14693 "broken": true 14694 }, 14695 "Metab": { 14696 "name": "Metab", 14697 "version": "1.4.1", 14698 "sha256": "0wi45k7lx7f7y8bfpa4d1lggnkxlwwyjgzw22xyfw9yj40ma5x9g", 14699 "depends": ["pander", "svDialogs", "xcms"], 14700 "broken": true 14701 }, 14702 "MethCP": { 14703 "name": "MethCP", 14704 "version": "1.11.0", 14705 "sha256": "099jaadjfalvxpwq3k630yrqa1dfbp8rqn2fahz1rsha3y5z9bys", 14706 "depends": ["BiocParallel", "bsseq", "DNAcopy", "DSS", "GenomeInfoDb", "GenomicRanges", "IRanges", "methylKit", "S4Vectors"], 14707 "broken": true 14708 }, 14709 "Mirsynergy": { 14710 "name": "Mirsynergy", 14711 "version": "1.6.0", 14712 "sha256": "0wb257fi5wygky6iqaxdhp8n3pxzknv1vy44ay55y0bal1nbkzwa", 14713 "depends": ["Matrix", "RColorBrewer", "ggplot2", "gridExtra", "igraph", "reshape", "scales"], 14714 "broken": true 14715 }, 14716 "MmPalateMiRNA": { 14717 "name": "MmPalateMiRNA", 14718 "version": "1.20.0", 14719 "sha256": "1salsb4askcv6xgzfwcwxkrr8qx7pjzqgljbw3ips2f4n6vqvyzj", 14720 "depends": ["Biobase", "lattice", "limma", "statmod", "vsn", "xtable"], 14721 "broken": true 14722 }, 14723 "MoPS": { 14724 "name": "MoPS", 14725 "version": "1.4.0", 14726 "sha256": "07bylvhv1wnzj3z2ycw4rb29mlz34sbpksl0sdk47q9f5cjgvlnf", 14727 "depends": ["Biobase"], 14728 "broken": true 14729 }, 14730 "MobilityTransformR": { 14731 "name": "MobilityTransformR", 14732 "version": "1.6.0", 14733 "sha256": "1292fk08zi1zf0hdj56vzdgv9h9nr16vmbzypqkam7lvqqnig49h", 14734 "depends": ["MetaboCoreUtils", "MSnbase", "Spectra", "xcms"], 14735 "broken": true 14736 }, 14737 "MotIV": { 14738 "name": "MotIV", 14739 "version": "1.26.0", 14740 "sha256": "0s26dklw8kav8lz0245as7y9znj4yfiknpmcgrdmm62rq04c11mp", 14741 "depends": ["BiocGenerics", "Biostrings", "IRanges", "S4Vectors", "lattice", "rGADEM"], 14742 "broken": true 14743 }, 14744 "NBSplice": { 14745 "name": "NBSplice", 14746 "version": "1.15.0", 14747 "sha256": "0yn7s7igshall34cflmdwvmknv8h1zdi6vg8svvcyn9fvzlgjdm8", 14748 "depends": ["BiocParallel", "car", "edgeR", "ggplot2", "MASS", "reshape2"], 14749 "broken": true 14750 }, 14751 "NGScopy": { 14752 "name": "NGScopy", 14753 "version": "1.4.0", 14754 "sha256": "1vs7mi0lb8jcm9yc0jz7rvdnj95fr06cf1jkb9p84pnm9vpn63d6", 14755 "depends": ["changepoint"], 14756 "broken": true 14757 }, 14758 "NanoStringQCPro": { 14759 "name": "NanoStringQCPro", 14760 "version": "1.2.0", 14761 "sha256": "1cbja0bi4sw3n4f1wkgbvmwh1hr49hhrybqxc6a7f8lvq11s28rf", 14762 "depends": ["AnnotationDbi", "Biobase", "NMF", "RColorBrewer", "knitr", "org_Hs_eg_db", "png"], 14763 "broken": true 14764 }, 14765 "NarrowPeaks": { 14766 "name": "NarrowPeaks", 14767 "version": "1.14.0", 14768 "sha256": "08nhw2ira3amjs9zl134afjqwi0hniq0g3mgmljjp1l0277b8acg", 14769 "depends": ["BiocGenerics", "CSAR", "GenomeInfoDb", "GenomicRanges", "ICSNP", "IRanges", "S4Vectors", "fda"], 14770 "broken": true 14771 }, 14772 "NeighborNet": { 14773 "name": "NeighborNet", 14774 "version": "1.18.0", 14775 "sha256": "046k1799wz77ww4jhf935pfz2637dmzy7p848iyjxj1yc5g51jq8", 14776 "depends": ["graph"], 14777 "broken": true 14778 }, 14779 "NeuCA": { 14780 "name": "NeuCA", 14781 "version": "1.10.0", 14782 "sha256": "0k5bqdrja3x238fyrd7dm5jm94igh25b0ipb2zj6scpa4m15n67l", 14783 "depends": ["SingleCellExperiment", "e1071", "kableExtra", "keras", "limma"], 14784 "broken": true 14785 }, 14786 "NxtIRFcore": { 14787 "name": "NxtIRFcore", 14788 "version": "1.6.0", 14789 "sha256": "1x3645v6ar8mpmyk6hd5w3m38496g68l2vdh80vh0hhlqlrp17n2", 14790 "depends": ["AnnotationHub", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "BSgenome", "data_table", "DelayedArray", "DelayedMatrixStats", "fst", "genefilter", "GenomeInfoDb", "GenomicRanges", "ggplot2", "HDF5Array", "IRanges", "magrittr", "NxtIRFdata", "plotly", "R_utils", "Rcpp", "RcppProgress", "rhdf5", "rtracklayer", "S4Vectors", "SummarizedExperiment", "zlibbioc"], 14791 "broken": true 14792 }, 14793 "ODER": { 14794 "name": "ODER", 14795 "version": "1.6.0", 14796 "sha256": "17c3hvdghli6i88yqy6dclzyad60s0d6y4hng6i4bycc9fnan41w", 14797 "depends": ["BiocFileCache", "BiocGenerics", "dasper", "data_table", "derfinder", "dplyr", "GenomeInfoDb", "GenomicRanges", "ggplot2", "ggpubr", "ggrepel", "IRanges", "magrittr", "megadepth", "plyr", "purrr", "rtracklayer", "S4Vectors", "stringr", "tibble"], 14798 "broken": true 14799 }, 14800 "OGSA": { 14801 "name": "OGSA", 14802 "version": "1.0.0", 14803 "sha256": "058lfd60w905jvhq99dsdcvl1q6h9dnwhqdqn942yr54jlkc7fjy", 14804 "depends": ["Biobase", "gplots", "limma"], 14805 "broken": true 14806 }, 14807 "OmicsLonDA": { 14808 "name": "OmicsLonDA", 14809 "version": "1.15.0", 14810 "sha256": "1kn26k0lnk7hgfzk1kh5bh41zkia8a4pzsfr35mbjrflcxmvgk2w", 14811 "depends": ["BiocGenerics", "BiocParallel", "ggplot2", "gss", "plyr", "pracma", "SummarizedExperiment", "zoo"], 14812 "broken": true 14813 }, 14814 "OmicsMLRepoR": { 14815 "name": "OmicsMLRepoR", 14816 "version": "1.2.0", 14817 "sha256": "0cfa80zylasvi7qbjiwsavl0yfn9ahji2sgzkfmi1lsbryppgyvc", 14818 "depends": ["BiocFileCache", "DiagrammeR", "data_tree", "dplyr", "jsonlite", "lubridate", "plyr", "readr", "rlang", "rols", "stringr", "tibble", "tidyr"], 14819 "broken": true 14820 }, 14821 "OmicsMarkeR": { 14822 "name": "OmicsMarkeR", 14823 "version": "1.2.0", 14824 "sha256": "1r4qn2p5fxyi6r9l7zgbga1n5wcy18whcvyx0cwrr7lawbzjn6yg", 14825 "depends": ["caTools", "caret", "data_table", "e1071", "foreach", "gbm", "glmnet", "pamr", "permute", "plyr", "randomForest"], 14826 "broken": true 14827 }, 14828 "OmnipathR": { 14829 "name": "OmnipathR", 14830 "version": "3.16.0", 14831 "sha256": "0l5zbb05f4rgykmppwfsdah1f6601zqq67jsd5y1ck76sl2hq4gc", 14832 "depends": ["RSQLite", "R_utils", "XML", "checkmate", "crayon", "curl", "digest", "dplyr", "fs", "httr2", "igraph", "jsonlite", "later", "logger", "lubridate", "magrittr", "progress", "purrr", "rappdirs", "readr", "readxl", "rlang", "rmarkdown", "rvest", "sessioninfo", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "vctrs", "withr", "xml2", "yaml", "zip"], 14833 "broken": true 14834 }, 14835 "OperaMate": { 14836 "name": "OperaMate", 14837 "version": "1.2.3", 14838 "sha256": "1zgqf2ywazrxc66l2x8280izrzanan51b8vz5jwy8i7gnrm4gaa0", 14839 "depends": ["fBasics", "gProfileR", "ggplot2", "gridExtra", "pheatmap", "reshape2", "stabledist"], 14840 "broken": true 14841 }, 14842 "OutlierD": { 14843 "name": "OutlierD", 14844 "version": "1.34.0", 14845 "sha256": "19wrakxv833r5jqcrk627kgn6pissna9xdfnhn389a0j50xb02is", 14846 "depends": ["Biobase", "quantreg"], 14847 "broken": true 14848 }, 14849 "PAPi": { 14850 "name": "PAPi", 14851 "version": "1.10.0", 14852 "sha256": "0q90yi4s3jln713cpylgan7fzw7c536kw7bqlnkkaw6rjj1k6vvg", 14853 "depends": ["KEGGREST", "svDialogs"], 14854 "broken": true 14855 }, 14856 "PAnnBuilder": { 14857 "name": "PAnnBuilder", 14858 "version": "1.34.0", 14859 "sha256": "086hgqx9svn1pfzcz6affj2p9kvjk5k4viqkmwknlk9smw53l40l", 14860 "depends": ["AnnotationDbi", "Biobase", "DBI", "RSQLite"], 14861 "broken": true 14862 }, 14863 "PCAtools": { 14864 "name": "PCAtools", 14865 "version": "2.20.0", 14866 "sha256": "0jik25f4rpmr8gjy22i2myjhgsgqgslfjfskhv5bgkmqwbn931ar", 14867 "depends": ["BH", "BiocParallel", "BiocSingular", "DelayedArray", "DelayedMatrixStats", "Matrix", "Rcpp", "beachmat", "cowplot", "dqrng", "ggplot2", "ggrepel", "lattice", "reshape2"], 14868 "broken": true 14869 }, 14870 "PCpheno": { 14871 "name": "PCpheno", 14872 "version": "1.32.0", 14873 "sha256": "023dkbi3r1bs9wiihx3rcdc1dx5w21pfmk0n3n7zan4k5jkz4rwx", 14874 "depends": ["AnnotationDbi", "Biobase", "Category", "GO_db", "GSEABase", "KEGG_db", "SLGI", "ScISI", "annotate", "graph", "ppiData", "ppiStats"], 14875 "broken": true 14876 }, 14877 "PERFect": { 14878 "name": "PERFect", 14879 "version": "1.14.0", 14880 "sha256": "0ygbirfnp122c8jzrig5cnm6rxyhz126ixl5ca49i13kizcv2ns9", 14881 "depends": ["fitdistrplus", "ggplot2", "Matrix", "phyloseq", "psych", "sn", "zoo"], 14882 "broken": true 14883 }, 14884 "PFP": { 14885 "name": "PFP", 14886 "version": "1.7.0", 14887 "sha256": "1328a73ggg7l1drjbmv67jcvlv83khn1k252mf81xj4gf213d0di", 14888 "depends": ["clusterProfiler", "ggplot2", "graph", "igraph", "KEGGgraph", "magrittr", "plyr", "tidyr"], 14889 "broken": true 14890 }, 14891 "PGA": { 14892 "name": "PGA", 14893 "version": "1.0.0", 14894 "sha256": "1s4ddjlnxh1waw1sm428lnaq655qfzlmabcjgdm95fi2cg66vs86", 14895 "depends": ["AnnotationDbi", "Biostrings", "GenomicFeatures", "GenomicRanges", "IRanges", "Nozzle_R1", "RCurl", "RSQLite", "Rsamtools", "VariantAnnotation", "biomaRt", "customProDB", "data_table", "ggplot2", "pheatmap", "rTANDEM", "rtracklayer", "stringr"], 14896 "broken": true 14897 }, 14898 "PGSEA": { 14899 "name": "PGSEA", 14900 "version": "1.44.0", 14901 "sha256": "0cfz479nlmbal4bs5ah12q6jpp7989xic59rml87i19bcbhz8z26", 14902 "depends": ["AnnotationDbi", "Biobase", "GO_db", "KEGG_db", "annaffy"], 14903 "broken": true 14904 }, 14905 "PICS": { 14906 "name": "PICS", 14907 "version": "2.51.0", 14908 "sha256": "1fchi92ka52902c4prscm85acw8f7sjihz2nx8lrc0qz421msdv7", 14909 "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools"], 14910 "broken": true 14911 }, 14912 "PING": { 14913 "name": "PING", 14914 "version": "2.51.0", 14915 "sha256": "1fhw93llsslbn13679iph91klzpaqzi953zbxl4n9c9r2sbngsc9", 14916 "depends": ["BSgenome", "BiocGenerics", "GenomicRanges", "Gviz", "IRanges", "PICS", "S4Vectors", "fda"], 14917 "broken": true 14918 }, 14919 "PSEA": { 14920 "name": "PSEA", 14921 "version": "1.4.0", 14922 "sha256": "1df2v472s2g4qcylvg9y5gahgjzq0m753j65736c8lc7g2zbpacp", 14923 "depends": ["Biobase", "MASS"], 14924 "broken": true 14925 }, 14926 "PSICQUIC": { 14927 "name": "PSICQUIC", 14928 "version": "1.8.3", 14929 "sha256": "1g3xkbgr3by0gd8ngiavxyy14ixdhrwcf5ka329k3129d816425p", 14930 "depends": ["BiocGenerics", "IRanges", "RCurl", "biomaRt", "httr", "plyr"], 14931 "broken": true 14932 }, 14933 "PanViz": { 14934 "name": "PanViz", 14935 "version": "1.6.0", 14936 "sha256": "1h4fxqxkaph5j3vkfhmmkhvmqa8czzdzxcg6f06v94hqf38i86i5", 14937 "depends": ["RColorBrewer", "colorspace", "data_table", "dplyr", "easycsv", "futile_logger", "igraph", "magrittr", "rentrez", "rlang", "stringr", "tibble", "tidyr"], 14938 "broken": true 14939 }, 14940 "PanVizGenerator": { 14941 "name": "PanVizGenerator", 14942 "version": "1.22.0", 14943 "sha256": "0rhx2jc5kc9bl00v16frh8b4075n0jqn4s37pkvqp3ypcbqws32d", 14944 "depends": ["igraph", "jsonlite", "pcaMethods", "shiny"], 14945 "broken": true 14946 }, 14947 "Pbase": { 14948 "name": "Pbase", 14949 "version": "0.10.0", 14950 "sha256": "02b2vw63gwssy6bz8v6dvfmz2ak5pa7wzz341nrbr3mwv0k27j4q", 14951 "depends": ["Biobase", "BiocGenerics", "Biostrings", "GenomicRanges", "Gviz", "IRanges", "MSnbase", "Pviz", "Rcpp", "S4Vectors", "biomaRt", "cleaver", "mzID", "mzR", "rtracklayer"], 14952 "broken": true 14953 }, 14954 "PhenStat": { 14955 "name": "PhenStat", 14956 "version": "2.44.0", 14957 "sha256": "0gzhfy6mz3dazwy9hcb8ffgsfry6r4byl2a8b9qkir8ymv3q6s2p", 14958 "depends": ["MASS", "car", "corrplot", "ggplot2", "graph", "knitr", "lme4", "logistf", "msgps", "nlme", "nortest", "pingr", "reshape"], 14959 "broken": true 14960 }, 14961 "Pi": { 14962 "name": "Pi", 14963 "version": "2.14.0", 14964 "sha256": "16jh7p3f6nk2hwvp44b9sas1dl618m520xj553x9dkaj77jmzp6d", 14965 "depends": ["BiocGenerics", "caret", "dplyr", "GenomeInfoDb", "GenomicRanges", "ggnetwork", "ggplot2", "ggrepel", "glmnet", "igraph", "IRanges", "lattice", "MASS", "Matrix", "osfr", "plot3D", "purrr", "randomForest", "RCircos", "readr", "ROCR", "scales", "supraHex", "tibble", "tidyr"], 14966 "broken": true 14967 }, 14968 "Pigengene": { 14969 "name": "Pigengene", 14970 "version": "1.34.0", 14971 "sha256": "02f1p69ci15r3l52g3fxvb4mfn4ldpl3vkh9710ynfdbn67dg0r9", 14972 "depends": ["BiocStyle", "C50", "DBI", "DOSE", "GO_db", "MASS", "ReactomePA", "Rgraphviz", "WGCNA", "bnlearn", "clusterProfiler", "dplyr", "gdata", "ggplot2", "graph", "impute", "matrixStats", "openxlsx", "partykit", "pheatmap", "preprocessCore"], 14973 "broken": true 14974 }, 14975 "Pirat": { 14976 "name": "Pirat", 14977 "version": "1.2.0", 14978 "sha256": "0wky524d2j1qw80rwr8v211bqfkrdn4zfp5v2j8d24p9x3f9iyj6", 14979 "depends": ["MASS", "S4Vectors", "SummarizedExperiment", "basilisk", "ggplot2", "invgamma", "progress", "reticulate"], 14980 "broken": true 14981 }, 14982 "PloGO2": { 14983 "name": "PloGO2", 14984 "version": "1.14.0", 14985 "sha256": "0r0zf8dfb4pv4hv5fp5v61i3q5bnzwxws1v3cnx7l64b0hjl2ffi", 14986 "depends": ["GO_db", "GOstats", "httr", "lattice", "openxlsx", "xtable"], 14987 "broken": true 14988 }, 14989 "PoTRA": { 14990 "name": "PoTRA", 14991 "version": "1.13.0", 14992 "sha256": "1a32d1wndb24pxza3h53yddj9z2clff5srny2k00pbbfq1h99mjf", 14993 "depends": ["BiocGenerics", "graph", "graphite", "igraph", "org_Hs_eg_db"], 14994 "broken": true 14995 }, 14996 "Polyfit": { 14997 "name": "Polyfit", 14998 "version": "1.4.0", 14999 "sha256": "0rhs81hclz59nqirpp9y5n7qmg343s260n1gv8ma3c8j2jicb333", 15000 "depends": ["DESeq"], 15001 "broken": true 15002 }, 15003 "PrecisionTrialDrawer": { 15004 "name": "PrecisionTrialDrawer", 15005 "version": "1.11.0", 15006 "sha256": "1miw8rj1zn1xv97dkgs66k9g21i6gp3j2m1l1akysskczgam3i2c", 15007 "depends": ["BiocParallel", "biomaRt", "brglm", "data_table", "DT", "GenomicRanges", "ggplot2", "ggrepel", "googleVis", "httr", "IRanges", "jsonlite", "LowMACAAnnotation", "magrittr", "matrixStats", "RColorBrewer", "reshape2", "S4Vectors", "shiny", "shinyBS", "stringr", "XML"], 15008 "broken": true 15009 }, 15010 "Prize": { 15011 "name": "Prize", 15012 "version": "1.0.0", 15013 "sha256": "1a9hvhpa29ns7lhzmdqjlasp6rwrzng8klaw9cz54vdvc7al49wn", 15014 "depends": ["diagram", "ggplot2", "gplots", "matrixcalc", "reshape2", "stringr"], 15015 "broken": true 15016 }, 15017 "ProCoNA": { 15018 "name": "ProCoNA", 15019 "version": "1.8.0", 15020 "sha256": "0j0ld484cd98304fncyixi86qnxh72m8s83xxyk8c81kf7lzvhw1", 15021 "depends": ["BiocGenerics", "GOstats", "MSnbase", "WGCNA", "flashClust"], 15022 "broken": true 15023 }, 15024 "ProteomicsAnnotationHubData": { 15025 "name": "ProteomicsAnnotationHubData", 15026 "version": "1.0.1", 15027 "sha256": "1wxx6mq1xs7l24p82rs0wsmfxhrjx6nv1m7wf73i33vrcy83g2i6", 15028 "depends": ["AnnotationHub", "AnnotationHubData", "Biobase", "BiocInstaller", "Biostrings", "GenomeInfoDb", "MSnbase", "RCurl", "mzR"], 15029 "broken": true 15030 }, 15031 "PubScore": { 15032 "name": "PubScore", 15033 "version": "1.8.0", 15034 "sha256": "18bmzvv6mxrdlh297i29q24vi5rc4x2mjaryi5asiki186x0hy8d", 15035 "depends": ["dplyr", "ggplot2", "ggrepel", "igraph", "intergraph", "network", "progress", "rentrez", "sna"], 15036 "broken": true 15037 }, 15038 "QUALIFIER": { 15039 "name": "QUALIFIER", 15040 "version": "1.14.1", 15041 "sha256": "1h87y2q8x4ri6sv7nbppzpqa96m99mijq1739h8cfab5wmi0bcl5", 15042 "depends": ["Biobase", "MASS", "XML", "data_table", "flowCore", "flowViz", "flowWorkspace", "hwriter", "lattice", "latticeExtra", "ncdfFlow", "reshape"], 15043 "broken": true 15044 }, 15045 "QuartPAC": { 15046 "name": "QuartPAC", 15047 "version": "1.2.0", 15048 "sha256": "0nx3a9jsp2rq61jszm6kgpbqi9m5jkqfvk94npp7nk3qwhfi00j8", 15049 "depends": ["GraphPAC", "SpacePAC", "data_table", "iPAC"], 15050 "broken": true 15051 }, 15052 "R453Plus1Toolbox": { 15053 "name": "R453Plus1Toolbox", 15054 "version": "1.58.0", 15055 "sha256": "1jc585yid6s9aw2if073hqi50wgmlr7g4pkdwvgrcsck45g7llfg", 15056 "depends": ["BSgenome", "Biobase", "BiocGenerics", "Biostrings", "GenomicRanges", "IRanges", "R2HTML", "Rsamtools", "S4Vectors", "ShortRead", "SummarizedExperiment", "TeachingDemos", "VariantAnnotation", "XVector", "biomaRt", "pwalign", "xtable"], 15057 "broken": true 15058 }, 15059 "RBioinf": { 15060 "name": "RBioinf", 15061 "version": "1.68.0", 15062 "sha256": "1q58rgg9mwnj47r945gpnpgdrp2hpkhfmgrs8w8hrqv718v2dx58", 15063 "depends": ["graph"], 15064 "broken": true 15065 }, 15066 "RCytoscape": { 15067 "name": "RCytoscape", 15068 "version": "1.20.1", 15069 "sha256": "1ymbj8xlny9bsbcxyvg9si7v2rlc7bw3sq0424bsfc92l3as0rjj", 15070 "depends": ["BiocGenerics", "graph"], 15071 "broken": true 15072 }, 15073 "RDAVIDWebService": { 15074 "name": "RDAVIDWebService", 15075 "version": "1.8.0", 15076 "sha256": "1f92a80zksp90wlj2iymdf20hqkbp1aw7mdb7w5r19zckskcrg1m", 15077 "depends": ["Category", "GO_db", "GOstats", "RBGL", "ggplot2", "graph", "rJava"], 15078 "broken": true 15079 }, 15080 "RGMQL": { 15081 "name": "RGMQL", 15082 "version": "1.24.0", 15083 "sha256": "1p7s17i18ql3b8yvg6pmcz62ql18ncd3hqk0rganmahfbd91idby", 15084 "depends": ["BiocGenerics", "GenomicRanges", "RGMQLlib", "S4Vectors", "data_table", "dplyr", "glue", "httr", "plyr", "rJava", "rtracklayer", "xml2"], 15085 "broken": true 15086 }, 15087 "RGalaxy": { 15088 "name": "RGalaxy", 15089 "version": "1.14.0", 15090 "sha256": "1g63kmfywmnjammifjkqiy8cnqvb77d2x4yff8bgz2ib60gyqm14", 15091 "depends": ["Biobase", "BiocGenerics", "XML", "digest", "optparse", "roxygen2"], 15092 "broken": true 15093 }, 15094 "RIPAT": { 15095 "name": "RIPAT", 15096 "version": "1.10.0", 15097 "sha256": "154a79xyihxkg3sbwxz9ch0ixqlqv9gwkpsv88i55c75qyzkx2sm", 15098 "depends": ["biomaRt", "GenomicRanges", "ggplot2", "IRanges", "karyoploteR", "openxlsx", "plyr", "regioneR", "rtracklayer", "stringr"], 15099 "broken": true 15100 }, 15101 "RIPSeeker": { 15102 "name": "RIPSeeker", 15103 "version": "1.10.0", 15104 "sha256": "09pr25pf488vdim3k6mvbvqqyxhl2dfs4y699x8xyhym34c74xcj", 15105 "depends": ["GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "SummarizedExperiment", "rtracklayer"], 15106 "broken": true 15107 }, 15108 "RLSeq": { 15109 "name": "RLSeq", 15110 "version": "1.5.2", 15111 "sha256": "0nhip321gbv6phwdwi3qkbmhnfh7fhb9md6xs4lklskwkkrd7s1q", 15112 "depends": ["AnnotationHub", "aws_s3", "callr", "caretEnsemble", "circlize", "ComplexHeatmap", "dplyr", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "ggplot2", "ggplotify", "ggprism", "pheatmap", "RColorBrewer", "regioneR", "rtracklayer", "valr", "VennDiagram"], 15113 "broken": true 15114 }, 15115 "RNASeqR": { 15116 "name": "RNASeqR", 15117 "version": "1.16.0", 15118 "sha256": "0m7d3mm644n81630v2m6vv7798x3rjshb9jcp63xq631j1wmk63i", 15119 "depends": ["ballgown", "Biostrings", "clusterProfiler", "corrplot", "DESeq2", "DOSE", "edgeR", "factoextra", "FactoMineR", "ggplot2", "gridExtra", "org_Hs_eg_db", "org_Sc_sgd_db", "pathview", "PerformanceAnalytics", "pheatmap", "rafalib", "reshape2", "reticulate", "Rsamtools", "stringr", "systemPipeR", "systemPipeRdata"], 15120 "broken": true 15121 }, 15122 "RNAdecay": { 15123 "name": "RNAdecay", 15124 "version": "1.28.0", 15125 "sha256": "10d1ciz37rxgkbi2hnqqq2cqkwrfflx1gcyjb5gl0zl8076rvy3m", 15126 "depends": ["TMB", "ggplot2", "gplots", "nloptr", "scales"], 15127 "broken": true 15128 }, 15129 "RNAinteract": { 15130 "name": "RNAinteract", 15131 "version": "1.18.0", 15132 "sha256": "0v7hz20nsc2dkb4xjzdhib2rj8k9zkn2c71rhg46b6hy3jxrm7m1", 15133 "depends": ["Biobase", "ICS", "ICSNP", "RColorBrewer", "abind", "cellHTS2", "geneplotter", "gplots", "hwriter", "lattice", "latticeExtra", "limma", "locfit", "splots"], 15134 "broken": true 15135 }, 15136 "RNAither": { 15137 "name": "RNAither", 15138 "version": "2.18.7", 15139 "sha256": "1mgm6y5ijlw3rpfi0vkdlw0zrfd4ciz3qmmp42vykmm8c5jsjc0x", 15140 "depends": ["RankProd", "biomaRt", "car", "geneplotter", "limma", "prada", "splots", "topGO"], 15141 "broken": true 15142 }, 15143 "RNAprobR": { 15144 "name": "RNAprobR", 15145 "version": "1.2.0", 15146 "sha256": "017sc7ba5kw55rc74acv3i5i0mg7h5hblaqxy4j2ln6iqm1h38fi", 15147 "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "Rsamtools", "plyr", "rtracklayer"], 15148 "broken": true 15149 }, 15150 "RWebServices": { 15151 "name": "RWebServices", 15152 "version": "1.34.0", 15153 "sha256": "05czankzfvgsfrs2am8dkglzcix22s7gc4bgci0a66x8z31dlkx0", 15154 "depends": ["RCurl", "SJava", "TypeInfo"], 15155 "broken": true 15156 }, 15157 "RamiGO": { 15158 "name": "RamiGO", 15159 "version": "1.16.0", 15160 "sha256": "12mwfcljw323aqpzc4z5hl2h5qy51bpi5z59x4hx8inw3vc3n55y", 15161 "depends": ["RCurl", "RCytoscape", "graph", "gsubfn", "igraph", "png"], 15162 "broken": true 15163 }, 15164 "RandomWalkRestartMH": { 15165 "name": "RandomWalkRestartMH", 15166 "version": "1.22.0", 15167 "sha256": "0mvh22p0dliwapdgbl5r93dpjdfnvnxdv5ig3y9gd2ndn32h1cyc", 15168 "depends": ["igraph", "Matrix"], 15169 "broken": true 15170 }, 15171 "Rariant": { 15172 "name": "Rariant", 15173 "version": "1.6.2", 15174 "sha256": "1jf8p5i6jqlniwrmsk6ajcrf6j637cx267nvb2742yd1jzfm5yy3", 15175 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SomaticSignatures", "VGAM", "VariantAnnotation", "dplyr", "exomeCopy", "ggbio", "ggplot2", "reshape2", "shiny"], 15176 "broken": true 15177 }, 15178 "Rcade": { 15179 "name": "Rcade", 15180 "version": "1.12.0", 15181 "sha256": "08q62agkyb810b0hfvs9vb9rh0ls8zrz83558xprijjizrkg9cg2", 15182 "depends": ["GenomicRanges", "Rsamtools", "S4Vectors", "baySeq", "plotrix", "rgl"], 15183 "broken": true 15184 }, 15185 "Rchemcpp": { 15186 "name": "Rchemcpp", 15187 "version": "2.8.0", 15188 "sha256": "0zz9s3zvxgs6mpiq085zy20sqajyx1645cz3848h2l0w1w5m6lga", 15189 "depends": ["ChemmineR", "Rcpp"], 15190 "broken": true 15191 }, 15192 "RchyOptimyx": { 15193 "name": "RchyOptimyx", 15194 "version": "2.10.0", 15195 "sha256": "0cmyjyr3dn8df9ss4zhhm6y1lhf68msl5br070x01i8kgh4dagky", 15196 "depends": ["Rgraphviz", "flowType", "graph", "sfsmisc"], 15197 "broken": true 15198 }, 15199 "ReQON": { 15200 "name": "ReQON", 15201 "version": "1.16.0", 15202 "sha256": "1j79vmhk34argysbjyxcsmfjsplkxq4cn8gprm6min1v08xzryg0", 15203 "depends": ["Rsamtools", "rJava", "seqbias"], 15204 "broken": true 15205 }, 15206 "ReactomeContentService4R": { 15207 "name": "ReactomeContentService4R", 15208 "version": "1.12.0", 15209 "sha256": "1qqrkki9v3ggwqv88n7w3wp50y4gxvkixrg1sad23vl08jd0rkl6", 15210 "depends": ["data_table", "doParallel", "foreach", "httr", "jsonlite", "magick"], 15211 "broken": true 15212 }, 15213 "ReactomeGraph4R": { 15214 "name": "ReactomeGraph4R", 15215 "version": "1.12.0", 15216 "sha256": "17xkrqyp5wdsdd0gpplsk3qfsr8sgf1ap0vz6v34xlhbmzdq3rs8", 15217 "depends": ["ReactomeContentService4R", "data_table", "doParallel", "foreach", "getPass", "jsonlite", "magrittr", "neo4r", "purrr", "rlang"], 15218 "broken": true 15219 }, 15220 "RefNet": { 15221 "name": "RefNet", 15222 "version": "1.6.1", 15223 "sha256": "0l0krjjk1jld7z5zy6k3z6m2qkqd86yj92xfck75q3bq3jm96h0j", 15224 "depends": ["AnnotationHub", "BiocGenerics", "IRanges", "PSICQUIC", "RCurl", "shiny"], 15225 "broken": true 15226 }, 15227 "RefPlus": { 15228 "name": "RefPlus", 15229 "version": "1.40.0", 15230 "sha256": "13qlm4smaafx1x78wn959wc1rm4wns7l6qgdmh1lg5khkrrh3x19", 15231 "depends": ["Biobase", "affy", "affyPLM", "preprocessCore"], 15232 "broken": true 15233 }, 15234 "RepViz": { 15235 "name": "RepViz", 15236 "version": "1.24.0", 15237 "sha256": "0822djg1akxrbz02wvvyn54b25nsrnhvwprnj4nj5bz981gcbn2p", 15238 "depends": ["GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "biomaRt"], 15239 "broken": true 15240 }, 15241 "Repitools": { 15242 "name": "Repitools", 15243 "version": "1.54.0", 15244 "sha256": "0k5vgpdnk4l0bi55dpidb2c6g13gyfia4xjzgsaliqaz3ss5w61x", 15245 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "DNAcopy", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "MASS", "Rsamtools", "Rsolnp", "S4Vectors", "cluster", "edgeR", "gplots", "rtracklayer"], 15246 "broken": true 15247 }, 15248 "Rfastp": { 15249 "name": "Rfastp", 15250 "version": "1.18.0", 15251 "sha256": "0lbfwgy5iv7jbbfgsijcyd7kfx7r5lpj3k5xypfdcx8cj9mm3ysb", 15252 "depends": ["Rcpp", "Rhtslib", "ggplot2", "reshape2", "rjson", "zlibbioc"], 15253 "broken": true 15254 }, 15255 "Rgin": { 15256 "name": "Rgin", 15257 "version": "1.15.0", 15258 "sha256": "1x5zj2d5rvsr2xh0ifpnrys9v91dal1xxhv5mmk16rs8wzwqpqba", 15259 "depends": ["RcppEigen"], 15260 "broken": true 15261 }, 15262 "Ringo": { 15263 "name": "Ringo", 15264 "version": "1.34.0", 15265 "sha256": "0r549n840sq9whaz8nk7rz3wardxc8jvwdni4bd5f7zzrhj0ynhl", 15266 "depends": ["Biobase", "BiocGenerics", "Matrix", "RColorBrewer", "genefilter", "lattice", "limma", "vsn"], 15267 "broken": true 15268 }, 15269 "Risa": { 15270 "name": "Risa", 15271 "version": "1.12.0", 15272 "sha256": "0s23fbdk1v1cg0c67vhkz53wava1swjig8fz8jsv8av0pqb0rg17", 15273 "depends": ["Biobase", "Rcpp", "affy", "biocViews", "xcms"], 15274 "broken": true 15275 }, 15276 "RmiR": { 15277 "name": "RmiR", 15278 "version": "1.26.0", 15279 "sha256": "1nnpr5jp5anbqbgyg53qqjhi49bibymc0l3yj6ar5d6csavrympb", 15280 "depends": ["DBI", "RmiR_Hs_miRNA"], 15281 "broken": true 15282 }, 15283 "Roleswitch": { 15284 "name": "Roleswitch", 15285 "version": "1.8.0", 15286 "sha256": "0libkpp9scrbakhzp030bx86f4np6ijn01r8xzn02f5106h23gz7", 15287 "depends": ["Biobase", "Biostrings", "DBI", "biomaRt", "microRNA", "plotrix", "pracma", "reshape"], 15288 "broken": true 15289 }, 15290 "Rolexa": { 15291 "name": "Rolexa", 15292 "version": "1.26.0", 15293 "sha256": "184v27zycmqnj4fpjgrxl3vcxxfxwkbfqdzm6wsyxixm93rmz7v4", 15294 "depends": ["Biostrings", "IRanges", "ShortRead", "mclust"], 15295 "broken": true 15296 }, 15297 "RpsiXML": { 15298 "name": "RpsiXML", 15299 "version": "2.12.0", 15300 "sha256": "0zlcr1f5sf98bwxakbmq33kniwlpxcc32z5fz7vqsasyv5vbz1ks", 15301 "depends": ["AnnotationDbi", "Biobase", "RBGL", "XML", "annotate", "graph", "hypergraph"], 15302 "broken": true 15303 }, 15304 "Rtreemix": { 15305 "name": "Rtreemix", 15306 "version": "1.69.0", 15307 "sha256": "1sw0linj05wz2f9ax5809mcl1l7h16nvdk8xxl2pwgv78jkfzq8h", 15308 "depends": ["Biobase", "Hmisc", "graph"], 15309 "broken": true 15310 }, 15311 "SAGx": { 15312 "name": "SAGx", 15313 "version": "1.44.0", 15314 "sha256": "0rrw1y80ybpskwvcdbyqq8m4d17sz07bv9gpa27rvfq2sy4znsk6", 15315 "depends": ["Biobase", "multtest"], 15316 "broken": true 15317 }, 15318 "SARC": { 15319 "name": "SARC", 15320 "version": "1.6.0", 15321 "sha256": "04g3pq9az8jfffgq19y8lzlhjrwi7gjlynfcpxpqsy8dk3gw5fwj", 15322 "depends": ["DescTools", "GenomicFeatures", "GenomicRanges", "IRanges", "RColorBrewer", "RaggedExperiment", "data_table", "ggplot2", "gridExtra", "gtable", "metap", "multtest", "plotly", "plyranges", "reshape2", "scales", "tidyverse"], 15323 "broken": true 15324 }, 15325 "SCATE": { 15326 "name": "SCATE", 15327 "version": "1.10.0", 15328 "sha256": "1fkswn9xlbr4mrnr62yzk51dri7rzbvf28whh7qhdfxgyvavw439", 15329 "depends": ["GenomicAlignments", "GenomicRanges", "mclust", "preprocessCore", "Rtsne", "SCATEData", "splines2", "xgboost"], 15330 "broken": true 15331 }, 15332 "SEPA": { 15333 "name": "SEPA", 15334 "version": "1.0.0", 15335 "sha256": "1hvkz3pyp8qkq1mjw9wl426db6n3ay05bx2djkdpvpbai4fjwgvc", 15336 "depends": ["ggplot2", "org_Hs_eg_db", "org_Mm_eg_db", "reshape2", "segmented", "shiny", "topGO"], 15337 "broken": true 15338 }, 15339 "SEPIRA": { 15340 "name": "SEPIRA", 15341 "version": "1.20.0", 15342 "sha256": "1yhlm6l9jv8fhdhnhpj7r8cdpnrp1la287x85gcssqjnv5v4k047", 15343 "depends": ["corpcor", "limma"], 15344 "broken": true 15345 }, 15346 "SGCP": { 15347 "name": "SGCP", 15348 "version": "1.8.0", 15349 "sha256": "0jagx4ygl1sz32l4hskqn87qmnpqwdjj2y0basa07gapny3df879", 15350 "depends": ["DescTools", "GO_db", "GOstats", "RColorBrewer", "RSpectra", "Rgraphviz", "SummarizedExperiment", "annotate", "caret", "dplyr", "expm", "genefilter", "ggplot2", "ggridges", "graph", "openxlsx", "org_Hs_eg_db", "plyr", "reshape2", "xtable"], 15351 "broken": true 15352 }, 15353 "SISPA": { 15354 "name": "SISPA", 15355 "version": "1.0.0", 15356 "sha256": "01kf83hlc7qyyxr4dx86m9vc16cydrkw4sajs2ikpn2fnrqkx6z1", 15357 "depends": ["GSVA", "changepoint", "data_table", "ggplot2", "plyr"], 15358 "broken": true 15359 }, 15360 "SJava": { 15361 "name": "SJava", 15362 "version": "0.96.0", 15363 "sha256": "17qvrd8n0vrn9fn9p31s2bhzf6064hnf89c54hbx3flzki73waaz", 15364 "depends": [], 15365 "broken": true 15366 }, 15367 "SLGI": { 15368 "name": "SLGI", 15369 "version": "1.30.0", 15370 "sha256": "1pardqmvmi4877q09n3379wq57pyqla53s8gxvygrqny2drb5crj", 15371 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GO_db", "ScISI", "lattice"], 15372 "broken": true 15373 }, 15374 "SMAP": { 15375 "name": "SMAP", 15376 "version": "1.34.0", 15377 "sha256": "07mdnmirsbz8m5zky169q2mqdn1sdh1nlx8qsgdf8h0n0vcs2h3z", 15378 "depends": [], 15379 "broken": true 15380 }, 15381 "SNPchip": { 15382 "name": "SNPchip", 15383 "version": "2.16.0", 15384 "sha256": "1fxskvkzn0mfcg2zjs2r2fr0pifrha54a15vbxxcawy4pggf7fdv", 15385 "depends": ["Biobase", "GenomeInfoDb", "GenomicRanges", "IRanges", "SummarizedExperiment", "foreach", "lattice", "oligoClasses"], 15386 "broken": true 15387 }, 15388 "SQLDataFrame": { 15389 "name": "SQLDataFrame", 15390 "version": "1.22.0", 15391 "sha256": "1hhllinhlb4byhjizkh68lk7rjxwgg1w7s4ngd99dlws814gav1z", 15392 "depends": ["BiocGenerics", "DBI", "DelayedArray", "RSQLite", "S4Vectors", "duckdb"], 15393 "broken": true 15394 }, 15395 "SQUADD": { 15396 "name": "SQUADD", 15397 "version": "1.20.0", 15398 "sha256": "1nxf68waqnm9jaj0r8z1499kw5c6l1sykj38wikcc39bsyy23kxm", 15399 "depends": ["RColorBrewer"], 15400 "broken": true 15401 }, 15402 "SSPA": { 15403 "name": "SSPA", 15404 "version": "2.10.0", 15405 "sha256": "1835g6chjrl1kz5zc710jy0lx04b84khk2kx981ga6rmlihn5xyc", 15406 "depends": ["lattice", "limma", "qvalue"], 15407 "broken": true 15408 }, 15409 "STAN": { 15410 "name": "STAN", 15411 "version": "1.4.0", 15412 "sha256": "0phrznzv3n9nvjbxb172ywxcc6dfjz2gw21w4nzxiwcjaf3kg841", 15413 "depends": ["Rsolnp"], 15414 "broken": true 15415 }, 15416 "STROMA4": { 15417 "name": "STROMA4", 15418 "version": "1.24.0", 15419 "sha256": "1x3zgxkcck8ffh89mql45cp54c94n64kf9x6dan9wl24bj3x869f", 15420 "depends": ["Biobase", "BiocParallel", "cluster", "matrixStats"], 15421 "broken": true 15422 }, 15423 "STdeconvolve": { 15424 "name": "STdeconvolve", 15425 "version": "1.8.0", 15426 "sha256": "0pyyxmh4bnavsdw6riv72y5m8l53mfr0lpiy9mh0qn57rlmw5fr9", 15427 "depends": ["BiocParallel", "Matrix", "clue", "ggplot2", "mgcv", "reshape2", "scatterpie", "slam", "topicmodels", "viridis"], 15428 "broken": true 15429 }, 15430 "SVM2CRM": { 15431 "name": "SVM2CRM", 15432 "version": "1.2.0", 15433 "sha256": "06jhyvq3j35skvkf57iqfphypsv43k12i0wybhhvx4wjsdrrhmwq", 15434 "depends": ["AnnotationDbi", "GenomicRanges", "IRanges", "LiblineaR", "ROCR", "SVM2CRMdata", "mclust", "pls", "rtracklayer", "squash", "verification", "zoo"], 15435 "broken": true 15436 }, 15437 "ScISI": { 15438 "name": "ScISI", 15439 "version": "1.42.0", 15440 "sha256": "0bmpl2zaalwxhhc9vj9v3x8ig6hbj4lrbfl2dxmivgsh1hqvbcli", 15441 "depends": ["AnnotationDbi", "GO_db", "RpsiXML", "annotate", "apComplex", "org_Sc_sgd_db"], 15442 "broken": true 15443 }, 15444 "ScreenR": { 15445 "name": "ScreenR", 15446 "version": "1.10.0", 15447 "sha256": "10mbdr4bf4pv8m8d6smppr6yrcsdk1dkx87qb9rr6fqvf3xwvdsq", 15448 "depends": ["dplyr", "edgeR", "ggplot2", "ggvenn", "limma", "magrittr", "patchwork", "purrr", "rlang", "scales", "stringr", "tibble", "tidyr", "tidyselect"], 15449 "broken": true 15450 }, 15451 "SigFuge": { 15452 "name": "SigFuge", 15453 "version": "1.46.0", 15454 "sha256": "0x9px4mm24r2ffw1vd26rdm0ibv0023amsjhda59gkwxdgppkgj7", 15455 "depends": ["GenomicRanges", "ggplot2", "matlab", "reshape", "sigclust"], 15456 "broken": true 15457 }, 15458 "SimBindProfiles": { 15459 "name": "SimBindProfiles", 15460 "version": "1.8.0", 15461 "sha256": "1cyqlzb6vykxndslwvmj9sn7hzrq3lqjwsmvkvl7ivfigrslg142", 15462 "depends": ["Biobase", "Ringo", "limma", "mclust"], 15463 "broken": true 15464 }, 15465 "SomatiCA": { 15466 "name": "SomatiCA", 15467 "version": "2.1.0", 15468 "sha256": "1a4c8hnl93mnqmm9abc2njcqrlynzbsf39im2gi3ypyjnzabs7m8", 15469 "depends": ["DNAcopy", "GenomicRanges", "IRanges", "doParallel", "foreach", "lars", "mvtnorm", "rebmix", "sn"], 15470 "broken": true 15471 }, 15472 "SpacePAC": { 15473 "name": "SpacePAC", 15474 "version": "1.8.0", 15475 "sha256": "11szjavnv8b3sdqdzda3vsx3rbzmnzdimm4b37lm3rfqzrs14qhc", 15476 "depends": ["iPAC"], 15477 "broken": true 15478 }, 15479 "SpidermiR": { 15480 "name": "SpidermiR", 15481 "version": "1.32.0", 15482 "sha256": "07s421c8ashww8x99ac18fy1lvjl4zmm3jsz0fggw1gvii172c1x", 15483 "depends": ["AnnotationDbi", "gdata", "httr", "igraph", "miRNAtap", "miRNAtap_db", "org_Hs_eg_db"], 15484 "broken": true 15485 }, 15486 "StarBioTrek": { 15487 "name": "StarBioTrek", 15488 "version": "1.28.0", 15489 "sha256": "0cpgn0zcimg18yybfgrjzdczsinvx6n81jjm850gbi76ararq8sc", 15490 "depends": ["AnnotationDbi", "e1071", "ggplot2", "graphite", "igraph", "MLmetrics", "reshape2", "ROCR", "SpidermiR"], 15491 "broken": true 15492 }, 15493 "Starr": { 15494 "name": "Starr", 15495 "version": "1.26.0", 15496 "sha256": "0ra9x1kzr0r2wa1ihapzmldq0fdr91rfbbglmzjnq92wrw6rvkd2", 15497 "depends": ["MASS", "Ringo", "affxparser", "affy", "pspline", "zlibbioc"], 15498 "broken": true 15499 }, 15500 "SummarizedBenchmark": { 15501 "name": "SummarizedBenchmark", 15502 "version": "2.20.0", 15503 "sha256": "16gzlkyf76fcd46ck417sxh86smivmaggqvyg0v9v0f4jac7610g", 15504 "depends": ["BiocGenerics", "BiocParallel", "crayon", "digest", "dplyr", "ggplot2", "mclust", "rlang", "S4Vectors", "sessioninfo", "stringr", "SummarizedExperiment", "tibble", "tidyr", "UpSetR"], 15505 "broken": true 15506 }, 15507 "Sushi": { 15508 "name": "Sushi", 15509 "version": "1.8.0", 15510 "sha256": "1ldvv1028chnh8ng85534k924cgdmzqb3i18z6xpacsjgg5k7s7l", 15511 "depends": ["biomaRt", "zoo"], 15512 "broken": true 15513 }, 15514 "SwimR": { 15515 "name": "SwimR", 15516 "version": "1.8.0", 15517 "sha256": "0vwjrpm4qbhc8afv0zj0al3rv06izp649kz8h3pb1yixw4bwrxg8", 15518 "depends": ["R2HTML", "gplots", "signal"], 15519 "broken": true 15520 }, 15521 "TCGAbiolinksGUI": { 15522 "name": "TCGAbiolinksGUI", 15523 "version": "1.23.0", 15524 "sha256": "16757szccczlv1q35y1cnmlkr12s46f63z7ijffpb15q85xlaqdx", 15525 "depends": ["caret", "clusterProfiler", "colourpicker", "data_table", "downloader", "DT", "ELMER", "ggplot2", "ggrepel", "maftools", "pathview", "plotly", "readr", "sesame", "shiny", "shinyBS", "shinydashboard", "shinyFiles", "shinyjs", "stringr", "SummarizedExperiment", "TCGAbiolinks", "TCGAbiolinksGUI_data"], 15526 "broken": true 15527 }, 15528 "TDARACNE": { 15529 "name": "TDARACNE", 15530 "version": "1.20.0", 15531 "sha256": "0jf89s2bnz8psd7vqh3l29ch5mb2ilky2jmv8db4kcqaw9157kn8", 15532 "depends": ["Biobase", "Rgraphviz"], 15533 "broken": true 15534 }, 15535 "TNBC_CMS": { 15536 "name": "TNBC.CMS", 15537 "version": "1.18.0", 15538 "sha256": "1syygq9br5icbjbmi1kq9gs7g3bw1vzmy8mlf8ga2rk1lw6ika90", 15539 "depends": ["e1071", "forestplot", "GGally", "ggplot2", "ggpubr", "GSVA", "pheatmap", "pracma", "quadprog", "R_utils", "RColorBrewer", "SummarizedExperiment", "survival"], 15540 "broken": true 15541 }, 15542 "TSRchitect": { 15543 "name": "TSRchitect", 15544 "version": "1.20.0", 15545 "sha256": "1v9zz8ny9rwkyz98cv49l9ilh68h8mvm2x44n8i8rvjayc50zi9i", 15546 "depends": ["AnnotationHub", "BiocGenerics", "BiocParallel", "dplyr", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "gtools", "IRanges", "readxl", "Rsamtools", "rtracklayer", "S4Vectors", "SummarizedExperiment"], 15547 "broken": true 15548 }, 15549 "TSSi": { 15550 "name": "TSSi", 15551 "version": "1.16.2", 15552 "sha256": "0lvvzhm0npm9hc7n9rw9ipqgp7kgyvciapai0y8l4r3c07wh8nbs", 15553 "depends": ["Biobase", "BiocGenerics", "Hmisc", "IRanges", "S4Vectors", "minqa", "plyr"], 15554 "broken": true 15555 }, 15556 "TarSeqQC": { 15557 "name": "TarSeqQC", 15558 "version": "1.0.3", 15559 "sha256": "06a9kvyx73ysllid9mafgyp1czhyf06gxma1b6bkyksingpgnb68", 15560 "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "cowplot", "ggplot2", "openxlsx", "plyr", "reshape2"], 15561 "broken": true 15562 }, 15563 "TimeSeriesExperiment": { 15564 "name": "TimeSeriesExperiment", 15565 "version": "1.13.0", 15566 "sha256": "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c", 15567 "depends": ["DESeq2", "dplyr", "dynamicTreeCut", "edgeR", "ggplot2", "Hmisc", "limma", "magrittr", "proxy", "S4Vectors", "SummarizedExperiment", "tibble", "tidyr", "vegan", "viridis"], 15568 "broken": true 15569 }, 15570 "TimiRGeN": { 15571 "name": "TimiRGeN", 15572 "version": "1.11.0", 15573 "sha256": "104j3rdl1mfklqvpsr753zlplr001cqbkphbhf2xrcfw8si7bgr2", 15574 "depends": ["biomaRt", "clusterProfiler", "dplyr", "FreqProf", "ggdendro", "gghighlight", "ggplot2", "gplots", "gtools", "igraph", "Mfuzz", "MultiAssayExperiment", "RCy3", "readxl", "reshape2", "rWikiPathways", "scales", "stringr", "tidyr"], 15575 "broken": true 15576 }, 15577 "TitanCNA": { 15578 "name": "TitanCNA", 15579 "version": "1.45.0", 15580 "sha256": "19znhy9gd40fcv3m1zx6kdh178f74j88rb5pkrdv53q48vcq68l3", 15581 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "VariantAnnotation", "data_table", "dplyr", "foreach"], 15582 "broken": true 15583 }, 15584 "ToPASeq": { 15585 "name": "ToPASeq", 15586 "version": "1.4.0", 15587 "sha256": "18fwifmih7x4wr7s3nr8qwvxbp0a33qj39sfwkvhr97jqdggb78j", 15588 "depends": ["AnnotationDbi", "Biobase", "DESeq", "DESeq2", "GenomicRanges", "KEGGgraph", "RBGL", "R_utils", "Rcpp", "Rgraphviz", "TeachingDemos", "clipper", "doParallel", "edgeR", "fields", "gRbase", "graph", "graphite", "limma", "locfit", "qpgraph"], 15589 "broken": true 15590 }, 15591 "TraRe": { 15592 "name": "TraRe", 15593 "version": "1.5.0", 15594 "sha256": "06w5rk2wjam5dhiya9n6kjbjahw4i46cb05zvakcy0f8gwrvb9ic", 15595 "depends": ["BiocParallel", "dqrng", "ggplot2", "glmnet", "gplots", "gtools", "hash", "igraph", "matrixStats", "pvclust", "R_utils", "SummarizedExperiment"], 15596 "broken": true 15597 }, 15598 "TransView": { 15599 "name": "TransView", 15600 "version": "1.14.0", 15601 "sha256": "02as66pzhgls2papji5mqpaczvdfpi6af0mafip8i9hj06z41wci", 15602 "depends": ["GenomicRanges", "IRanges", "Rsamtools", "gplots", "zlibbioc"], 15603 "broken": true 15604 }, 15605 "Travel": { 15606 "name": "Travel", 15607 "version": "1.6.0", 15608 "sha256": "074v9hl4gzy8081mlas3mjaplchjrmk2bl4f5nkdjclh46xf3wgg", 15609 "depends": ["Rcpp"], 15610 "broken": true 15611 }, 15612 "TypeInfo": { 15613 "name": "TypeInfo", 15614 "version": "1.36.0", 15615 "sha256": "0f0cllsf0pw2bgvq9fhfksqsxb2820js5y125vhcr0ns5kcvi07y", 15616 "depends": [], 15617 "broken": true 15618 }, 15619 "Vega": { 15620 "name": "Vega", 15621 "version": "1.18.0", 15622 "sha256": "0f7rzzckd69xbnism0v7jl0dly55lwj30nla7yj88qqalnb7ajzs", 15623 "depends": [], 15624 "broken": true 15625 }, 15626 "XBSeq": { 15627 "name": "XBSeq", 15628 "version": "1.0.2", 15629 "sha256": "01h3hj4mm7dr16vwbra5iazrgar9nbh2gs2gklyx0wqjfzm3gj49", 15630 "depends": ["Biobase", "DESeq2", "Delaporte", "dplyr", "ggplot2", "locfit", "magrittr", "matrixStats", "pracma"], 15631 "broken": true 15632 }, 15633 "XCIR": { 15634 "name": "XCIR", 15635 "version": "1.7.0", 15636 "sha256": "0n42pw01wv1sk06hby9kwijx6zwaw4lrlpsa0wlkrkf323slkllw", 15637 "depends": ["biomaRt", "data_table", "ggplot2", "IRanges", "readxl", "S4Vectors", "seqminer", "VariantAnnotation"], 15638 "broken": true 15639 }, 15640 "XNAString": { 15641 "name": "XNAString", 15642 "version": "1.15.0", 15643 "sha256": "1q50h6fvkc8fr5kvz3whvfiqx3fkxi8m7r1h459sqk362j9pydrj", 15644 "depends": ["BSgenome", "Biostrings", "GenomicRanges", "IRanges", "Rcpp", "S4Vectors", "data_table", "formattable", "future_apply", "pwalign", "stringi", "stringr"], 15645 "broken": true 15646 }, 15647 "affyPara": { 15648 "name": "affyPara", 15649 "version": "1.30.0", 15650 "sha256": "14g7xrzsqqsr2h20nv000dd3v71wq18bq78r345w29fs53kipxxd", 15651 "depends": ["affy", "affyio", "aplpack", "snow", "vsn"], 15652 "broken": true 15653 }, 15654 "affyQCReport": { 15655 "name": "affyQCReport", 15656 "version": "1.48.0", 15657 "sha256": "0cw6z8idar5qa9y3svrm5fdimdamb2xjjj59d107h2in7bvgni7j", 15658 "depends": ["Biobase", "RColorBrewer", "affy", "affyPLM", "genefilter", "lattice", "simpleaffy", "xtable"], 15659 "broken": true 15660 }, 15661 "affypdnn": { 15662 "name": "affypdnn", 15663 "version": "1.44.0", 15664 "sha256": "1av7a8w86wcslbl3q2zbnga8rww3n7dmwdywq4fm86pbmwh1jz9v", 15665 "depends": ["affy"], 15666 "broken": true 15667 }, 15668 "alpine": { 15669 "name": "alpine", 15670 "version": "1.26.0", 15671 "sha256": "1md4m9ln1mpxf7d2h7jnsjyi4zrviiqn9fzk1gkz2n6qj7jwpqbb", 15672 "depends": ["Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "graph", "IRanges", "RBGL", "Rsamtools", "S4Vectors", "speedglm", "stringr", "SummarizedExperiment"], 15673 "broken": true 15674 }, 15675 "alsace": { 15676 "name": "alsace", 15677 "version": "1.6.0", 15678 "sha256": "1vrwi2rkccgiwgshz5rxyr55dl7awbh1drbhhsrbpjsbzxwmiv4a", 15679 "depends": ["ALS", "ptw"], 15680 "broken": true 15681 }, 15682 "ampliQueso": { 15683 "name": "ampliQueso", 15684 "version": "1.8.0", 15685 "sha256": "0v21y2nd0qwnag0n6h0krr9c0vpv6ig89d0jsi58x3pi5m0mypip", 15686 "depends": ["DESeq", "VariantAnnotation", "doParallel", "edgeR", "foreach", "genefilter", "ggplot2", "gplots", "knitr", "rgl", "rnaSeqMap", "samr", "statmod", "xtable"], 15687 "broken": true 15688 }, 15689 "amplican": { 15690 "name": "amplican", 15691 "version": "1.30.0", 15692 "sha256": "0y5bknkn6l32bk2ia0dv3c8pp2dx2n83iwhbqh0l13jajv8j1csd", 15693 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "Matrix", "Rcpp", "S4Vectors", "ShortRead", "cluster", "data_table", "dplyr", "ggplot2", "ggthemes", "gridExtra", "gtable", "knitr", "matrixStats", "pwalign", "rmarkdown", "stringr", "waffle"], 15694 "broken": true 15695 }, 15696 "arrayQualityMetrics": { 15697 "name": "arrayQualityMetrics", 15698 "version": "3.64.0", 15699 "sha256": "1kz2d40wx2ksy9dz1z3wylcj7y7ad9z8xphsnz39j02m4g5mbvlp", 15700 "depends": ["Biobase", "Hmisc", "RColorBrewer", "XML", "affy", "affyPLM", "beadarray", "genefilter", "gridSVG", "hwriter", "lattice", "latticeExtra", "limma", "setRNG", "svglite", "vsn"], 15701 "broken": true 15702 }, 15703 "barcodetrackR": { 15704 "name": "barcodetrackR", 15705 "version": "1.16.0", 15706 "sha256": "1n2rj50gwqmqj5gs5d3asd3gcs0iv1rr1zh12s55lcsdxyfgp1ar", 15707 "depends": ["RColorBrewer", "S4Vectors", "SummarizedExperiment", "circlize", "cowplot", "dplyr", "ggdendro", "ggplot2", "ggridges", "magrittr", "plyr", "proxy", "rlang", "scales", "shiny", "tibble", "tidyr", "vegan", "viridis"], 15708 "broken": true 15709 }, 15710 "beadarray": { 15711 "name": "beadarray", 15712 "version": "2.58.0", 15713 "sha256": "0m9hmy4xn7q2v4ra95b9h08d0qh5qmjgqmg96vabyv46gn5i7qp4", 15714 "depends": ["AnnotationDbi", "BeadDataPackR", "Biobase", "BiocGenerics", "GenomicRanges", "IRanges", "ggplot2", "hexbin", "illuminaio", "limma", "reshape2"], 15715 "broken": true 15716 }, 15717 "beadarraySNP": { 15718 "name": "beadarraySNP", 15719 "version": "1.36.0", 15720 "sha256": "1dj5zi9lkyq5lgrcmr08cjdv3ysfa6p9zc8jza8mm6vy14qsl5ah", 15721 "depends": ["Biobase", "quantsmooth"], 15722 "broken": true 15723 }, 15724 "benchdamic": { 15725 "name": "benchdamic", 15726 "version": "1.14.3", 15727 "sha256": "0xc05qghdr2xynf5gk695xbpb5hj0wrfcjps34h8cqd249by2dk6", 15728 "depends": ["ALDEx2", "ANCOMBC", "BiocParallel", "DESeq2", "GUniFrac", "MAST", "MGLM", "Maaslin2", "MicrobiomeStat", "NOISeq", "RColorBrewer", "Seurat", "SummarizedExperiment", "TreeSummarizedExperiment", "corncob", "cowplot", "dearseq", "edgeR", "ggdendro", "ggplot2", "ggridges", "limma", "lme4", "maaslin3", "metagenomeSeq", "microbiome", "mixOmics", "phyloseq", "plyr", "reshape2", "tidytext", "zinbwave"], 15729 "broken": true 15730 }, 15731 "betr": { 15732 "name": "betr", 15733 "version": "1.26.0", 15734 "sha256": "1rs2xajrac3a4sk88i7zq3v849969iw0k8wmpbc0ihw9m4ljb0sx", 15735 "depends": ["Biobase", "limma", "mvtnorm"], 15736 "broken": true 15737 }, 15738 "bgafun": { 15739 "name": "bgafun", 15740 "version": "1.32.0", 15741 "sha256": "1wakjjdcgzl9snsa9i1f7kk0ppwiccxmznd93yawvjk74gqwnkp3", 15742 "depends": ["ade4", "made4", "seqinr"], 15743 "broken": true 15744 }, 15745 "bgx": { 15746 "name": "bgx", 15747 "version": "1.36.0", 15748 "sha256": "1x0i4llp6yrfybp7lwqwc7kb1s12dl8a0nwymhjd3fkfv5lslfbx", 15749 "depends": ["Biobase", "affy", "gcrma"], 15750 "broken": true 15751 }, 15752 "bigPint": { 15753 "name": "bigPint", 15754 "version": "1.15.0", 15755 "sha256": "1r9gr5f9as09ifagal5k7713h95qjw508cf8ny3j1jmqd24v6xhs", 15756 "depends": ["DelayedArray", "dplyr", "GGally", "ggplot2", "gridExtra", "hexbin", "Hmisc", "htmlwidgets", "plotly", "plyr", "RColorBrewer", "reshape", "shiny", "shinycssloaders", "shinydashboard", "stringr", "SummarizedExperiment", "tidyr"], 15757 "broken": true 15758 }, 15759 "bigmemoryExtras": { 15760 "name": "bigmemoryExtras", 15761 "version": "1.14.2", 15762 "sha256": "05ksk3phvh4wc3vgfj5bl1jfxhndia90bkq9s91wfjzcfkrd41q8", 15763 "depends": ["Biobase", "bigmemory"], 15764 "broken": true 15765 }, 15766 "biodbExpasy": { 15767 "name": "biodbExpasy", 15768 "version": "1.8.1", 15769 "sha256": "0n5avxhv5131122h18d3r2v9c64i3nb251hmz8hhc6chmk203fmj", 15770 "depends": ["R6", "biodb", "chk", "stringr"], 15771 "broken": true 15772 }, 15773 "biodbHmdb": { 15774 "name": "biodbHmdb", 15775 "version": "1.14.0", 15776 "sha256": "0xpc2dygjm8gy7612ggk2kgd599859l0i8qdjzx01vvchckkps5h", 15777 "depends": ["R6", "Rcpp", "biodb", "testthat", "zip"], 15778 "broken": true 15779 }, 15780 "biodbKegg": { 15781 "name": "biodbKegg", 15782 "version": "1.10.2", 15783 "sha256": "0rwxbg3ij5rg3agzsxib7f80b05ar40xnql2krl44c3n43yqkwyw", 15784 "depends": ["R6", "biodb", "chk", "lifecycle"], 15785 "broken": true 15786 }, 15787 "biodbLipidmaps": { 15788 "name": "biodbLipidmaps", 15789 "version": "1.10.0", 15790 "sha256": "1p181kwy9q8jj4m7flg71pqn7h6865hbwha4n6j2qki830vym6rv", 15791 "depends": ["R6", "biodb", "lifecycle"], 15792 "broken": true 15793 }, 15794 "biodbMirbase": { 15795 "name": "biodbMirbase", 15796 "version": "1.5.0", 15797 "sha256": "17clip9l8as9pz390bqgj07jxp1rijis2f5hj53s6vqaqmiyz4il", 15798 "depends": ["biodb", "chk", "R6", "stringr"], 15799 "broken": true 15800 }, 15801 "biodbNcbi": { 15802 "name": "biodbNcbi", 15803 "version": "1.12.0", 15804 "sha256": "19f37fgbhb22k27riklbdary3a1ybnm7drapfkss7grizwpa9d0x", 15805 "depends": ["R6", "XML", "biodb", "chk"], 15806 "broken": true 15807 }, 15808 "biodbNci": { 15809 "name": "biodbNci", 15810 "version": "1.12.0", 15811 "sha256": "10fyx0mdhllqlykhm3xnv59hw0ham27wgnswapk0a36rr804mfpj", 15812 "depends": ["R6", "Rcpp", "biodb", "chk", "testthat"], 15813 "broken": true 15814 }, 15815 "biodbUniprot": { 15816 "name": "biodbUniprot", 15817 "version": "1.14.0", 15818 "sha256": "1m27a7ngn4gwhj37vwg2mq5588q3cp85fcq5fjbjygi7l3d3pwg3", 15819 "depends": ["R6", "biodb"], 15820 "broken": true 15821 }, 15822 "biosvd": { 15823 "name": "biosvd", 15824 "version": "2.6.0", 15825 "sha256": "0mjkan7drib9v49dk3rnrkydm1dxfqimk5gk4jm9qv8kdfcjk0zh", 15826 "depends": ["Biobase", "BiocGenerics", "NMF"], 15827 "broken": true 15828 }, 15829 "birta": { 15830 "name": "birta", 15831 "version": "1.14.0", 15832 "sha256": "1pszpvmvjp1r0bwj7w9ws0y8xmb3yfmq5gifj9jwvgw2p7y718zr", 15833 "depends": ["Biobase", "MASS", "limma"], 15834 "broken": true 15835 }, 15836 "birte": { 15837 "name": "birte", 15838 "version": "1.6.1", 15839 "sha256": "08jkjlkjswz3x4sxw80xr9ck6277ag1gzv5y1dxh7aa6i644w48p", 15840 "depends": ["Biobase", "MASS", "Rcpp", "RcppArmadillo", "glmnet", "limma", "nem"], 15841 "broken": true 15842 }, 15843 "blima": { 15844 "name": "blima", 15845 "version": "1.42.0", 15846 "sha256": "0hsgd1zl3i2v4916c7dxlwlpm3affmgpb9s58p9rj1as3nvk6z9l", 15847 "depends": ["Biobase", "BiocGenerics", "Rcpp", "beadarray"], 15848 "broken": true 15849 }, 15850 "brainflowprobes": { 15851 "name": "brainflowprobes", 15852 "version": "1.16.0", 15853 "sha256": "06gga72ns7h9c6mdbvbj8afpkyizg7maazriilvaq433h6s1pgqb", 15854 "depends": ["Biostrings", "BSgenome_Hsapiens_UCSC_hg19", "bumphunter", "cowplot", "derfinder", "derfinderPlot", "GenomicRanges", "GenomicState", "ggplot2", "RColorBrewer"], 15855 "broken": true 15856 }, 15857 "branchpointer": { 15858 "name": "branchpointer", 15859 "version": "1.34.0", 15860 "sha256": "0n3linwha0lj65m72k7zm2bslxkdkjb1yqgs5ksdxrlziwmfs2nj", 15861 "depends": ["BSgenome_Hsapiens_UCSC_hg38", "Biostrings", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "biomaRt", "caret", "cowplot", "data_table", "gbm", "ggplot2", "kernlab", "plyr", "rtracklayer", "stringr"], 15862 "broken": true 15863 }, 15864 "bridge": { 15865 "name": "bridge", 15866 "version": "1.34.0", 15867 "sha256": "08lfbczaj7hkgqfsm060z56anx1yvsfwknzw40gq919k0zm9vfcf", 15868 "depends": ["rama"], 15869 "broken": true 15870 }, 15871 "broadSeq": { 15872 "name": "broadSeq", 15873 "version": "1.2.4", 15874 "sha256": "00xqpr915yhimmimbr43010ljdj7fiq613a3yq6haxvkqjpv83ri", 15875 "depends": ["BiocStyle", "DELocal", "DESeq2", "EBSeq", "NOISeq", "SummarizedExperiment", "clusterProfiler", "dplyr", "edgeR", "forcats", "genefilter", "ggplot2", "ggplotify", "ggpubr", "pheatmap", "plyr", "purrr", "sechm", "stringr"], 15876 "broken": true 15877 }, 15878 "caOmicsV": { 15879 "name": "caOmicsV", 15880 "version": "1.0.0", 15881 "sha256": "0162h17szpr98g4lgz5nypcrslk4103hdn5qdxfxv6frssn9l9g3", 15882 "depends": ["bc3net", "igraph"], 15883 "broken": true 15884 }, 15885 "ccmap": { 15886 "name": "ccmap", 15887 "version": "1.34.0", 15888 "sha256": "1khc7n1qpm7f4mpqy4qa74v03q581knig30hbvcd0a5x8gk8bvj3", 15889 "depends": ["AnnotationDbi", "BiocManager", "ccdata", "data_table", "doParallel", "foreach", "lsa", "xgboost"], 15890 "broken": true 15891 }, 15892 "cellGrowth": { 15893 "name": "cellGrowth", 15894 "version": "1.14.0", 15895 "sha256": "0d40kll2rkzijyk0d0xb9rzyck5r0hkybv0j1ba72g9kk2mdmz7z", 15896 "depends": ["lattice", "locfit"], 15897 "broken": true 15898 }, 15899 "cellHTS": { 15900 "name": "cellHTS", 15901 "version": "1.40.2", 15902 "sha256": "1cdzrmqr3fwxylc3m7g72bmc5iml266355i0mfdavp2q9y28kc85", 15903 "depends": ["Biobase", "RColorBrewer", "genefilter", "prada"], 15904 "broken": true 15905 }, 15906 "cellHTS2": { 15907 "name": "cellHTS2", 15908 "version": "2.34.1", 15909 "sha256": "068lqpxhy04fhpma8cbd79jwg0cifvg8qhav5a4p22dgmalvajw1", 15910 "depends": ["Biobase", "Category", "GSEABase", "RColorBrewer", "genefilter", "hwriter", "locfit", "prada", "splots", "vsn"], 15911 "broken": true 15912 }, 15913 "cellTree": { 15914 "name": "cellTree", 15915 "version": "1.27.0", 15916 "sha256": "0yfr59fcbdj03ikkpvw1qcxqrjbkz7nkfmb5m1xr4k9qs39bq9sb", 15917 "depends": ["gplots", "igraph", "maptpx", "slam", "topGO", "topicmodels", "xtable"], 15918 "broken": true 15919 }, 15920 "charm": { 15921 "name": "charm", 15922 "version": "2.16.1", 15923 "sha256": "00bvgpj705v9jb43skj5iljjf131dnz90n2rc1yww6s2kh4qqppm", 15924 "depends": ["BSgenome", "Biobase", "Biostrings", "IRanges", "RColorBrewer", "SQN", "ff", "fields", "genefilter", "gtools", "limma", "nor1mix", "oligo", "oligoClasses", "preprocessCore", "siggenes", "sva"], 15925 "broken": true 15926 }, 15927 "chevreulShiny": { 15928 "name": "chevreulShiny", 15929 "version": "1.0.0", 15930 "sha256": "0cl1wx66wk2l206yjvhnjmdacn3vbci6gzxii5djqiisr8zp42ml", 15931 "depends": ["ComplexHeatmap", "DBI", "DT", "DataEditR", "EnhancedVolcano", "RSQLite", "S4Vectors", "SingleCellExperiment", "alabaster_base", "chevreulPlot", "chevreulProcess", "clustree", "dplyr", "fs", "future", "ggplot2", "ggplotify", "patchwork", "plotly", "purrr", "rappdirs", "readr", "scales", "shiny", "shinyFiles", "shinyWidgets", "shinydashboard", "shinyhelper", "shinyjs", "stringr", "tibble", "tidyr", "tidyselect", "waiter", "wiggleplotr"], 15932 "broken": true 15933 }, 15934 "chimera": { 15935 "name": "chimera", 15936 "version": "1.12.0", 15937 "sha256": "11arbg6c76rx4zyylp6ga8ygx8890h0pkg4ciwhy4xc8x1smmq7r", 15938 "depends": ["AnnotationDbi", "BSgenome_Hsapiens_UCSC_hg19", "Biobase", "GenomicAlignments", "GenomicRanges", "Homo_sapiens", "Rsamtools", "TxDb_Hsapiens_UCSC_hg19_knownGene"], 15939 "broken": true 15940 }, 15941 "chroGPS": { 15942 "name": "chroGPS", 15943 "version": "1.14.0", 15944 "sha256": "0i0hrf38sjsay6r6zh69cy6xki17cjw427szq4h7770jlphiq8n1", 15945 "depends": ["Biobase", "ICSNP", "IRanges", "MASS", "changepoint", "cluster"], 15946 "broken": true 15947 }, 15948 "chromstaR": { 15949 "name": "chromstaR", 15950 "version": "1.32.0", 15951 "sha256": "071aipwk1awr71hvzflps49dzp83p12zm1pbyx4l8d2v3wbj0dlz", 15952 "depends": ["BiocGenerics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "bamsignals", "chromstaRData", "doParallel", "foreach", "ggplot2", "mvtnorm", "reshape2"], 15953 "broken": true 15954 }, 15955 "chromswitch": { 15956 "name": "chromswitch", 15957 "version": "1.22.0", 15958 "sha256": "007wa8980hkpja33ph3b3fjsjrf91cnwc0a7y4014k8xxmmgfdh7", 15959 "depends": ["Biobase", "BiocParallel", "cluster", "dplyr", "GenomicRanges", "gplots", "IRanges", "lazyeval", "magrittr", "matrixStats", "NMF", "rtracklayer", "S4Vectors", "tidyr"], 15960 "broken": true 15961 }, 15962 "cisPath": { 15963 "name": "cisPath", 15964 "version": "1.47.0", 15965 "sha256": "0q9fk47jwsbslyqjx6b4qr65xvxappr63xkvm2a6458r3hxaf41y", 15966 "depends": [], 15967 "broken": true 15968 }, 15969 "clonotypeR": { 15970 "name": "clonotypeR", 15971 "version": "1.8.0", 15972 "sha256": "1fj00hrxijkn002ixa7kn07jq94mlsgz99xr3sapzg0jqacgp9q0", 15973 "depends": [], 15974 "broken": true 15975 }, 15976 "coMET": { 15977 "name": "coMET", 15978 "version": "1.2.1", 15979 "sha256": "017sjx9wamyg6jglnbw1ynkbnp9idj9142jhkqvy8xji6kqh5xpk", 15980 "depends": ["GenomicRanges", "Gviz", "IRanges", "S4Vectors", "biomaRt", "corrplot", "ggbio", "ggplot2", "gridExtra", "hash", "psych", "rtracklayer", "trackViewer"], 15981 "broken": true 15982 }, 15983 "coRNAi": { 15984 "name": "coRNAi", 15985 "version": "1.20.0", 15986 "sha256": "05jv85jbb5lz0x0cmg52sn6gnsscyq939yyk6ll9061bx51as7cv", 15987 "depends": ["MASS", "cellHTS2", "gplots", "lattice", "limma", "locfit"], 15988 "broken": true 15989 }, 15990 "cobindR": { 15991 "name": "cobindR", 15992 "version": "1.8.0", 15993 "sha256": "06nckxm5hz6c336p5fvfmccfzdri68qcmagkyjg7nnfsyl66fri1", 15994 "depends": ["BSgenome", "BiocGenerics", "Biostrings", "IRanges", "biomaRt", "gmp", "gplots", "mclust", "seqinr", "yaml"], 15995 "broken": true 15996 }, 15997 "coexnet": { 15998 "name": "coexnet", 15999 "version": "1.19.1", 16000 "sha256": "0zw8a8pqmajqnv5n6i7fn7krwax81sd4c6wqm4zr61fy2blqzv3h", 16001 "depends": ["acde", "affy", "Biobase", "GEOquery", "igraph", "limma", "minet", "rmarkdown", "siggenes", "STRINGdb", "SummarizedExperiment", "vsn"], 16002 "broken": true 16003 }, 16004 "comapr": { 16005 "name": "comapr", 16006 "version": "1.12.0", 16007 "sha256": "0ggks950kr5c8x4l0479lh882r4svxagaq2y65hv26x23c03hzkx", 16008 "depends": ["BiocParallel", "GenomeInfoDb", "GenomicRanges", "Gviz", "IRanges", "Matrix", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "circlize", "dplyr", "foreach", "ggplot2", "gridExtra", "plotly", "plyr", "reshape2", "rlang", "scales", "tidyr"], 16009 "broken": true 16010 }, 16011 "compartmap": { 16012 "name": "compartmap", 16013 "version": "1.18.0", 16014 "sha256": "0lvgwnp5cgn96m9y4snpczfbfs72lxbaa36lnmwa7j07jy4s9108", 16015 "depends": ["BiocSingular", "DelayedArray", "DelayedMatrixStats", "GenomicRanges", "ggplot2", "HDF5Array", "Matrix", "RaggedExperiment", "reshape2", "RMTstat", "rtracklayer", "scales", "SummarizedExperiment"], 16016 "broken": true 16017 }, 16018 "conclus": { 16019 "name": "conclus", 16020 "version": "1.5.0", 16021 "sha256": "09rk73sxqxsy0zq07n67jxqbzb1rlxlj0phg6987szdjwxmag6jc", 16022 "depends": ["AnnotationDbi", "Biobase", "BiocFileCache", "biomaRt", "clusterProfiler", "dbscan", "doParallel", "dplyr", "factoextra", "foreach", "fpc", "GEOquery", "ggplot2", "gridExtra", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "rlang", "Rtsne", "scales", "scater", "scran", "SingleCellExperiment", "stringr", "SummarizedExperiment"], 16023 "broken": true 16024 }, 16025 "contiBAIT": { 16026 "name": "contiBAIT", 16027 "version": "1.30.0", 16028 "sha256": "1asyfx0mbg0pli2g533xmlppfw0s0f1y4vf2rfrnai4chsh1rh0k", 16029 "depends": ["BH", "BiocGenerics", "BiocParallel", "clue", "cluster", "colorspace", "data_table", "diagram", "DNAcopy", "exomeCopy", "GenomicAlignments", "GenomicFiles", "GenomicRanges", "ggplot2", "gplots", "gtools", "IRanges", "Rcpp", "reshape2", "Rsamtools", "rtracklayer", "S4Vectors", "TSP"], 16030 "broken": true 16031 }, 16032 "copynumber": { 16033 "name": "copynumber", 16034 "version": "1.10.0", 16035 "sha256": "1g03cy5inbhzhl5hj8vma34xm8lixilhalavjysp93bwg4dfskv6", 16036 "depends": ["BiocGenerics", "GenomicRanges", "IRanges", "S4Vectors"], 16037 "broken": true 16038 }, 16039 "crisprseekplus": { 16040 "name": "crisprseekplus", 16041 "version": "1.26.0", 16042 "sha256": "1ccz944jwlcnflrdh1aamfc5b03n6pys65b13f049f0x214vqg68", 16043 "depends": ["AnnotationDbi", "BiocManager", "BSgenome", "CRISPRseek", "DT", "GenomicFeatures", "GenomicRanges", "GUIDEseq", "hash", "shiny", "shinyjs"], 16044 "broken": true 16045 }, 16046 "crossmeta": { 16047 "name": "crossmeta", 16048 "version": "1.30.0", 16049 "sha256": "1ghgfby1rl3phldyipli550f0i289yanb0v4nzn5l1xnpkxaj6fa", 16050 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocManager", "DBI", "DT", "GEOquery", "RCurl", "RSQLite", "XML", "affxparser", "affy", "data_table", "edgeR", "fdrtool", "limma", "matrixStats", "metaMA", "miniUI", "oligo", "reader", "readxl", "shiny", "shinyBS", "shinyWidgets", "shinyjs", "shinypanel", "stringr", "sva", "tibble"], 16051 "broken": true 16052 }, 16053 "ctgGEM": { 16054 "name": "ctgGEM", 16055 "version": "1.7.0", 16056 "sha256": "0hmapz96r024r3bws1wf0spd0i81viyma859y9nn93jrwxscrcdb", 16057 "depends": ["Biobase", "BiocGenerics", "igraph", "Matrix", "monocle", "sincell", "SummarizedExperiment", "TSCAN"], 16058 "broken": true 16059 }, 16060 "cummeRbund": { 16061 "name": "cummeRbund", 16062 "version": "2.50.0", 16063 "sha256": "1i1zcrfizp4ix0bgx3gjbd4y4hj7dfs15j4ssh87kkx61y7x6yl8", 16064 "depends": ["Biobase", "BiocGenerics", "Gviz", "RSQLite", "S4Vectors", "fastcluster", "ggplot2", "plyr", "reshape2", "rtracklayer"], 16065 "broken": true 16066 }, 16067 "customProDB": { 16068 "name": "customProDB", 16069 "version": "1.48.0", 16070 "sha256": "1ixpq5fasq2n2f1rbwi1icnb6v96hakkv7kqsvzmp2lraxqh5lv0", 16071 "depends": ["AhoCorasickTrie", "AnnotationDbi", "Biostrings", "DBI", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "RCurl", "RSQLite", "Rsamtools", "S4Vectors", "VariantAnnotation", "biomaRt", "plyr", "rtracklayer", "stringr", "txdbmaker"], 16072 "broken": true 16073 }, 16074 "cytofQC": { 16075 "name": "cytofQC", 16076 "version": "1.8.0", 16077 "sha256": "13lcf0bldkccpgz5673cn2n64wqmwx98qpb9vzdlbin981pxr5ny", 16078 "depends": ["CATALYST", "EZtune", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "e1071", "flowCore", "gbm", "ggplot2", "hrbrthemes", "matrixStats", "randomForest", "rmarkdown", "ssc"], 16079 "broken": true 16080 }, 16081 "cytofkit": { 16082 "name": "cytofkit", 16083 "version": "1.2.4", 16084 "sha256": "1pgaw18m4z3az3b0d5d2wlvfq0ha80k5bc0vyjd9grlbwcpvs6nr", 16085 "depends": ["Biobase", "RANN", "Rcpp", "Rtsne", "VGAM", "doParallel", "e1071", "flowCore", "ggplot2", "gplots", "igraph", "pdist", "plyr", "reshape", "reshape2", "shiny", "vegan"], 16086 "broken": true 16087 }, 16088 "dandelionR": { 16089 "name": "dandelionR", 16090 "version": "1.0.2", 16091 "sha256": "0m8p003mgf03n69z0bcbid2insskg04vhhrvrppsciqcc9a4rbb4", 16092 "depends": ["BiocGenerics", "MASS", "Matrix", "RANN", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "bluster", "destiny", "igraph", "miloR", "purrr", "rlang", "spam", "uwot"], 16093 "broken": true 16094 }, 16095 "dasper": { 16096 "name": "dasper", 16097 "version": "1.9.0", 16098 "sha256": "095ldl40cay5n8lkp8y69lbmflhnbwm1b075s4zgpagn81awp0cn", 16099 "depends": ["basilisk", "BiocFileCache", "BiocParallel", "data_table", "dplyr", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "ggplot2", "ggpubr", "ggrepel", "IRanges", "magrittr", "megadepth", "plyranges", "readr", "reticulate", "rtracklayer", "S4Vectors", "stringr", "SummarizedExperiment", "tidyr"], 16100 "broken": true 16101 }, 16102 "dce": { 16103 "name": "dce", 16104 "version": "1.13.0", 16105 "sha256": "02gnlskfgn38fcf5mchp6ippcd2rj4cl4w7r08igaqyl02zy2x80", 16106 "depends": ["MASS", "Matrix", "Rgraphviz", "assertthat", "dplyr", "edgeR", "epiNEM", "expm", "ggplot2", "ggraph", "glm2", "glue", "graph", "graphite", "harmonicmeanp", "igraph", "logger", "magrittr", "metap", "mnem", "naturalsort", "org_Hs_eg_db", "pcalg", "ppcor", "purrr", "reshape2", "rlang", "shadowtext", "tidygraph", "tidyverse"], 16107 "broken": true 16108 }, 16109 "ddgraph": { 16110 "name": "ddgraph", 16111 "version": "1.14.0", 16112 "sha256": "0nmrz9cy7l31vym3fcc9m3dmgmbnd5r91p3fxpziaarphi27zszl", 16113 "depends": ["MASS", "RColorBrewer", "Rcpp", "bnlearn", "graph", "gtools", "pcalg", "plotrix"], 16114 "broken": true 16115 }, 16116 "debCAM": { 16117 "name": "debCAM", 16118 "version": "1.26.0", 16119 "sha256": "1sh8vbhgrkk1xfk139jxi88s2z70pnr4ji2pnb2gb3s5013zrhk8", 16120 "depends": ["Biobase", "BiocParallel", "NMF", "SummarizedExperiment", "apcluster", "corpcor", "geometry", "nnls", "pcaPP", "rJava"], 16121 "broken": true 16122 }, 16123 "deco": { 16124 "name": "deco", 16125 "version": "1.13.0", 16126 "sha256": "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw", 16127 "depends": ["ade4", "AnnotationDbi", "Biobase", "BiocParallel", "BiocStyle", "cluster", "foreign", "gdata", "ggplot2", "gplots", "gridExtra", "limma", "locfit", "made4", "RColorBrewer", "reshape2", "scatterplot3d", "sfsmisc", "SummarizedExperiment"], 16128 "broken": true 16129 }, 16130 "destiny": { 16131 "name": "destiny", 16132 "version": "3.22.0", 16133 "sha256": "01l01b6k55ifhppsp83scjf3f168r62xigz73s718ik8qbvirgqa", 16134 "depends": ["Biobase", "BiocGenerics", "Matrix", "RSpectra", "Rcpp", "RcppEigen", "RcppHNSW", "SingleCellExperiment", "SummarizedExperiment", "VIM", "ggplot2", "ggplot_multistats", "ggthemes", "irlba", "knn_covertree", "pcaMethods", "proxy", "rlang", "scales", "scatterplot3d", "smoother", "tidyr", "tidyselect"], 16135 "broken": true 16136 }, 16137 "dexus": { 16138 "name": "dexus", 16139 "version": "1.10.0", 16140 "sha256": "0hc28mkmnr37fmw6xw2cywla946gm0cxa8k4hi32d12cm9c24xqx", 16141 "depends": ["BiocGenerics"], 16142 "broken": true 16143 }, 16144 "diffloop": { 16145 "name": "diffloop", 16146 "version": "1.24.0", 16147 "sha256": "0v0jg9y08xzw775x2lm82ig1ag4wjf4z2l6a66zmk6qbn59dwj1g", 16148 "depends": ["Biobase", "biomaRt", "data_table", "dplyr", "edgeR", "foreach", "GenomeInfoDb", "GenomicRanges", "ggplot2", "IRanges", "limma", "locfit", "matrixStats", "pbapply", "plyr", "readr", "reshape2", "rtracklayer", "S4Vectors", "statmod", "Sushi"], 16149 "broken": true 16150 }, 16151 "domainsignatures": { 16152 "name": "domainsignatures", 16153 "version": "1.30.0", 16154 "sha256": "0rr5d57cjkp46qp2908vh3wyfdgiyaikdgbcxipizcv5a00nq0rx", 16155 "depends": ["AnnotationDbi", "KEGG_db", "biomaRt", "prada"], 16156 "broken": true 16157 }, 16158 "dpeak": { 16159 "name": "dpeak", 16160 "version": "1.12.0", 16161 "sha256": "1fx2rrcqmjckk5kk3mfa56b1393b2c8sf566q95d8zmlsvkl03w5", 16162 "depends": ["BSgenome", "IRanges", "MASS", "Rcpp"], 16163 "broken": true 16164 }, 16165 "drawProteins": { 16166 "name": "drawProteins", 16167 "version": "1.28.0", 16168 "sha256": "06fv2fhka123kj9rc2h0z07ym30wxk24fq8v0pzmf8gfyg4ywgfj", 16169 "depends": ["dplyr", "ggplot2", "httr", "readr", "tidyr"], 16170 "broken": true 16171 }, 16172 "dualKS": { 16173 "name": "dualKS", 16174 "version": "1.30.0", 16175 "sha256": "02j9l73brxa4fgsp9cbd3w7dxllvj744rby21dkfnw2c42rcxpvz", 16176 "depends": ["Biobase", "affy"], 16177 "broken": true 16178 }, 16179 "eegc": { 16180 "name": "eegc", 16181 "version": "1.26.0", 16182 "sha256": "0m67zjsq2xzk292rp0hdlj8lbfgci2dsdb5hmn4b591fqawwsqbb", 16183 "depends": ["AnnotationDbi", "clusterProfiler", "DESeq2", "DOSE", "edgeR", "ggplot2", "gplots", "igraph", "limma", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "R_utils", "S4Vectors", "sna", "wordcloud"], 16184 "broken": true 16185 }, 16186 "eisa": { 16187 "name": "eisa", 16188 "version": "1.22.0", 16189 "sha256": "0p3s6z7s4d165h4w5g1h273626h5j255c0hyjv5dlrdhr4ign7v6", 16190 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "Category", "DBI", "genefilter", "isa2"], 16191 "broken": true 16192 }, 16193 "enrichTF": { 16194 "name": "enrichTF", 16195 "version": "1.18.0", 16196 "sha256": "0lhmlxw7mpb76w2agm25v5qzxgf28wfw2xc0fnlqn2sbbfj295y9", 16197 "depends": ["BiocGenerics", "BSgenome", "clusterProfiler", "GenomeInfoDb", "GenomicRanges", "ggplot2", "ggpubr", "heatmap3", "IRanges", "JASPAR2018", "magrittr", "motifmatchr", "pipeFrame", "R_utils", "rmarkdown", "rtracklayer", "S4Vectors", "TFBSTools"], 16198 "broken": true 16199 }, 16200 "ensemblVEP": { 16201 "name": "ensemblVEP", 16202 "version": "1.10.3", 16203 "sha256": "1q9bzs9zqk2xv10jnq7571f8wgyi2l6zk6sgd4sja6fw82lrnmsy", 16204 "depends": ["BiocGenerics", "Biostrings", "GenomicRanges", "VariantAnnotation"], 16205 "broken": true 16206 }, 16207 "epigenomix": { 16208 "name": "epigenomix", 16209 "version": "1.48.1", 16210 "sha256": "05wvdfrgj2hpj8qm83k6jfbl4794zcafsh1g0d9bzd882f1n43bs", 16211 "depends": ["Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MCMCpack", "Rsamtools", "S4Vectors", "SummarizedExperiment", "beadarray"], 16212 "broken": true 16213 }, 16214 "epihet": { 16215 "name": "epihet", 16216 "version": "1.13.0", 16217 "sha256": "1p5sgb438yj6h0fv0v17dhz1pl32vai5zcbmgpgagrd5829a6a7r", 16218 "depends": ["data_table", "doParallel", "foreach", "GenomicRanges", "ggplot2", "igraph", "IRanges", "pheatmap", "qvalue", "ReactomePA", "Rtsne", "S4Vectors", "WGCNA"], 16219 "broken": true 16220 }, 16221 "erma": { 16222 "name": "erma", 16223 "version": "1.24.1", 16224 "sha256": "1s3b2a0iv3rl3sxq1sbqscq2h2gjz4d3vsg9phhnbk1xdhbhqi4d", 16225 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicFiles", "GenomicRanges", "Homo_sapiens", "IRanges", "S4Vectors", "SummarizedExperiment", "ggplot2", "rtracklayer", "shiny"], 16226 "broken": true 16227 }, 16228 "exomeCopy": { 16229 "name": "exomeCopy", 16230 "version": "1.16.0", 16231 "sha256": "09awyyfgs0k639nqrcrbq1k875qlyac1146w4ay6nxgijqy7iv82", 16232 "depends": ["GenomeInfoDb", "GenomicRanges", "IRanges", "Rsamtools"], 16233 "broken": true 16234 }, 16235 "exomePeak": { 16236 "name": "exomePeak", 16237 "version": "2.2.2", 16238 "sha256": "03xj0h1cgxzbp2fk830l771jmmcll1bq81xips8hjgng3ywz5m1a", 16239 "depends": ["GenomicAlignments", "GenomicFeatures", "Rsamtools", "rtracklayer"], 16240 "broken": true 16241 }, 16242 "exomePeak2": { 16243 "name": "exomePeak2", 16244 "version": "1.14.3", 16245 "sha256": "1hvz18hlvljbv0cmdlxzvsl2ysb5m0c5qq2y8jxzsby3zxlqplph", 16246 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "BSgenome", "DESeq2", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "IRanges", "magrittr", "mclust", "Rsamtools", "rtracklayer", "S4Vectors", "speedglm", "SummarizedExperiment"], 16247 "broken": true 16248 }, 16249 "explorase": { 16250 "name": "explorase", 16251 "version": "1.34.0", 16252 "sha256": "108p864qq8zh4x7p765ygrdkj4r0vm3s2fmi3scswkhcv3vjcjg3", 16253 "depends": ["limma"], 16254 "broken": true 16255 }, 16256 "facopy": { 16257 "name": "facopy", 16258 "version": "1.4.1", 16259 "sha256": "07ggz86c48rz8asqvfglrvsimnzh3ii43kzpm8ji6sd43i141650", 16260 "depends": ["DOSE", "FactoMineR", "GO_db", "GOstats", "IRanges", "MASS", "Rgraphviz", "annotate", "coin", "data_table", "facopy_annot", "ggplot2", "graphite", "gridExtra", "igraph", "nnet", "reshape2", "scales"], 16261 "broken": true 16262 }, 16263 "factR": { 16264 "name": "factR", 16265 "version": "1.10.0", 16266 "sha256": "131rmjl1awazpapmdag3kcjxjgb5gdxh2xvrvpvzhw45r4nd69v0", 16267 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "RCurl", "S4Vectors", "XML", "crayon", "data_table", "dplyr", "drawProteins", "ggplot2", "pbapply", "purrr", "rlang", "rtracklayer", "stringr", "tibble", "tidyr", "wiggleplotr"], 16268 "broken": true 16269 }, 16270 "famat": { 16271 "name": "famat", 16272 "version": "1.18.0", 16273 "sha256": "00fzbqa065z2si0yq4gvici4vfxwa8dwfyx077kc9d7a4z99b2wa", 16274 "depends": ["BiasedUrn", "DT", "GO_db", "KEGGREST", "clusterProfiler", "dplyr", "gprofiler2", "magrittr", "mgcv", "ontologyIndex", "org_Hs_eg_db", "plotly", "rWikiPathways", "reactome_db", "shiny", "shinyBS", "shinydashboard", "stringr", "tidyr"], 16275 "broken": true 16276 }, 16277 "farms": { 16278 "name": "farms", 16279 "version": "1.22.0", 16280 "sha256": "1jmx5rajm6fkhx5gfpwh8nsqw0plhfzy1bibvkdf83arxjjr6s59", 16281 "depends": ["Biobase", "MASS", "affy"], 16282 "broken": true 16283 }, 16284 "fcoex": { 16285 "name": "fcoex", 16286 "version": "1.13.0", 16287 "sha256": "085r5s5sqrj2701zk5kv3818ksxvxzd76lknzi6bk1svw4d3lsyc", 16288 "depends": ["clusterProfiler", "data_table", "dplyr", "FCBF", "ggplot2", "ggrepel", "igraph", "intergraph", "Matrix", "network", "pathwayPCA", "progress", "scales", "SingleCellExperiment", "sna", "stringr"], 16289 "broken": true 16290 }, 16291 "flipflop": { 16292 "name": "flipflop", 16293 "version": "1.8.2", 16294 "sha256": "1v4ihrmw0vphz0k0f37qy5k8zwa5g5cnj4agccjl4mqbvwiq4awh", 16295 "depends": ["GenomicRanges", "IRanges", "Matrix"], 16296 "broken": true 16297 }, 16298 "flowCL": { 16299 "name": "flowCL", 16300 "version": "1.8.0", 16301 "sha256": "064946w944gw7l0hizw974i21cahzvfj1xza8f7ay9rx2baz28sh", 16302 "depends": ["Rgraphviz"], 16303 "broken": true 16304 }, 16305 "flowFit": { 16306 "name": "flowFit", 16307 "version": "1.8.0", 16308 "sha256": "1fja1d5irh71a3rqdsbw5sb14ss2xmird6vxcps96r6s6rz2bra3", 16309 "depends": ["flowCore", "flowViz", "gplots", "kza", "minpack_lm"], 16310 "broken": true 16311 }, 16312 "flowMap": { 16313 "name": "flowMap", 16314 "version": "1.8.0", 16315 "sha256": "0rkdspl9lnasc8axlsx076g14pkgwrlz9nbxy0f1z67w991d823p", 16316 "depends": ["Matrix", "abind", "ade4", "doParallel", "reshape2", "scales"], 16317 "broken": true 16318 }, 16319 "flowQ": { 16320 "name": "flowQ", 16321 "version": "1.30.0", 16322 "sha256": "1yz0w0bpv98l319y8dw82qaykg6w70sxpzmhxdckwdqjpixq5sf5", 16323 "depends": ["BiocGenerics", "IRanges", "RColorBrewer", "bioDist", "flowCore", "flowViz", "geneplotter", "lattice", "latticeExtra", "mvoutlier", "outliers", "parody"], 16324 "broken": true 16325 }, 16326 "flowQB": { 16327 "name": "flowQB", 16328 "version": "1.14.0", 16329 "sha256": "1swsdqra8w8z27p2mv1q37ydak7rjifxm78h5x6mhv1vfq4faz12", 16330 "depends": ["Biobase", "MASS", "flowCore"], 16331 "broken": true 16332 }, 16333 "flowType": { 16334 "name": "flowType", 16335 "version": "2.8.2", 16336 "sha256": "0q7bk8pn71zyzc1m16rqimlyldnfj178k64vg0kw4yiwdjxlgdr4", 16337 "depends": ["BH", "Biobase", "Rcpp", "flowClust", "flowCore", "flowMeans", "flowMerge", "rrcov", "sfsmisc"], 16338 "broken": true 16339 }, 16340 "flowUtils": { 16341 "name": "flowUtils", 16342 "version": "1.34.0", 16343 "sha256": "0qba66cfsy8facvdpnl5jf71xwaqs3w6j2z0ph7c39zyng0nibwp", 16344 "depends": ["Biobase", "RUnit", "XML", "corpcor", "flowCore", "flowViz", "graph"], 16345 "broken": true 16346 }, 16347 "focalCall": { 16348 "name": "focalCall", 16349 "version": "1.4.0", 16350 "sha256": "1dqk0lda24lkhfsid15c6n121s63zbk6658za5qxqkxdd82z7axf", 16351 "depends": ["CGHcall"], 16352 "broken": true 16353 }, 16354 "gCMAP": { 16355 "name": "gCMAP", 16356 "version": "1.14.0", 16357 "sha256": "09dcaq0763kb399wh232n6r1s8qkj0c4zcmpjp6cz08w6n7lchgx", 16358 "depends": ["AnnotationDbi", "Biobase", "Category", "DESeq", "GSEABase", "GSEAlm", "Matrix", "annotate", "genefilter", "limma"], 16359 "broken": true 16360 }, 16361 "gCMAPWeb": { 16362 "name": "gCMAPWeb", 16363 "version": "1.10.0", 16364 "sha256": "00qx90gycqqca8b3brkl0bkckn7saqz9z38vinhjxlyaanc9v6ml", 16365 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GSEABase", "Rook", "annotate", "brew", "gCMAP", "hwriter", "yaml"], 16366 "broken": true 16367 }, 16368 "gINTomics": { 16369 "name": "gINTomics", 16370 "version": "1.4.0", 16371 "sha256": "04b1ksazr3l1b1k5rylmswzlfgz5xixgds2n10a1yiqwbbcjkn2p", 16372 "depends": ["AnnotationDbi", "BiocGenerics", "BiocParallel", "ComplexHeatmap", "DT", "GenomicFeatures", "GenomicRanges", "InteractiveComplexHeatmap", "MASS", "MethylMix", "MultiAssayExperiment", "OmnipathR", "RColorBrewer", "ReactomePA", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg38_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "biomaRt", "callr", "circlize", "clusterProfiler", "dplyr", "edgeR", "ggplot2", "ggridges", "ggtree", "ggvenn", "gtools", "limma", "org_Hs_eg_db", "org_Mm_eg_db", "plotly", "plyr", "randomForest", "reshape2", "shiny", "shiny_gosling", "shinydashboard", "shinyjs", "stringi", "stringr", "visNetwork"], 16373 "broken": true 16374 }, 16375 "gQTLBase": { 16376 "name": "gQTLBase", 16377 "version": "1.2.1", 16378 "sha256": "1a1ndjjp2zn1lsfahpvi3xhkdgwl5wk0bdm7kc92aidq50a2db42", 16379 "depends": ["BBmisc", "BatchJobs", "BiocGenerics", "GenomicFiles", "GenomicRanges", "S4Vectors", "bit", "doParallel", "ff", "foreach", "rtracklayer"], 16380 "broken": true 16381 }, 16382 "gQTLstats": { 16383 "name": "gQTLstats", 16384 "version": "1.2.0", 16385 "sha256": "1cwri36z85zyyr48dkkl7qkgbx9fpv7y38mbbm470adc7ac56zbv", 16386 "depends": ["AnnotationDbi", "BatchJobs", "Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment", "VariantAnnotation", "doParallel", "dplyr", "foreach", "gQTLBase", "gam", "ggplot2", "limma", "reshape2", "snpStats"], 16387 "broken": true 16388 }, 16389 "gaggle": { 16390 "name": "gaggle", 16391 "version": "1.38.0", 16392 "sha256": "0bl60nca27rkij061h6g16ddlkq29rb1wh5pr2hz87y74pmb8m2w", 16393 "depends": ["RUnit", "graph", "rJava"], 16394 "broken": true 16395 }, 16396 "gaia": { 16397 "name": "gaia", 16398 "version": "2.14.0", 16399 "sha256": "099imzsa7pghp7qbxjjnfrqc8zkn25wm5xj9jn40m9as11zxdrsx", 16400 "depends": [], 16401 "broken": true 16402 }, 16403 "gaucho": { 16404 "name": "gaucho", 16405 "version": "1.6.0", 16406 "sha256": "1c1aaidhdv9rr2v3q6832q0ajc3g7l4gfx1rhf27kv4pn1j5s23s", 16407 "depends": ["GA", "Rgraphviz", "graph", "png"], 16408 "broken": true 16409 }, 16410 "geecc": { 16411 "name": "geecc", 16412 "version": "1.4.0", 16413 "sha256": "00dkp4ldnpadvw6fdva0gg0m843j7i667r0i33c9dsrjfc7k7z8q", 16414 "depends": ["MASS", "gplots"], 16415 "broken": true 16416 }, 16417 "genbankr": { 16418 "name": "genbankr", 16419 "version": "1.27.0", 16420 "sha256": "0fv87cf2y10ijlb0g1x9g9wh95qyljqb1c7k1ihbnjcg36xkh8lc", 16421 "depends": ["Biobase", "BiocGenerics", "Biostrings", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "rtracklayer", "S4Vectors", "VariantAnnotation"], 16422 "broken": true 16423 }, 16424 "genoCN": { 16425 "name": "genoCN", 16426 "version": "1.59.0", 16427 "sha256": "1fyyq6759p7pz8ajgkn08clpvygm8b25jlf8m3sgrvw62kwcilxl", 16428 "depends": [], 16429 "broken": true 16430 }, 16431 "genoset": { 16432 "name": "genoset", 16433 "version": "1.24.0", 16434 "sha256": "0xxh23sdb5qjfh97a2psp70zb54zx40x8501bpp7gzgqbfn1wf7w", 16435 "depends": ["Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "SummarizedExperiment"], 16436 "broken": true 16437 }, 16438 "genotypeeval": { 16439 "name": "genotypeeval", 16440 "version": "1.0.0", 16441 "sha256": "1clljhqy57yy0ss9700zfnsgnby3dism8z2682xjhzzprg049cx4", 16442 "depends": ["BiocGenerics", "BiocParallel", "GenomeInfoDb", "GenomicRanges", "IRanges", "VariantAnnotation", "ggplot2", "rtracklayer"], 16443 "broken": true 16444 }, 16445 "genphen": { 16446 "name": "genphen", 16447 "version": "1.24.0", 16448 "sha256": "1m60qagcxviix4zjzfhvrwchbjq2clss6mivb8q07bcq369yw1b8", 16449 "depends": ["Biostrings", "doParallel", "e1071", "foreach", "ranger", "Rcpp", "rPref", "rstan"], 16450 "broken": true 16451 }, 16452 "gespeR": { 16453 "name": "gespeR", 16454 "version": "1.2.0", 16455 "sha256": "0s8lndwwqkkkiyqzi8xpqz6clzjrkmkkrh2f1ch80hvfj83rb89d", 16456 "depends": ["Biobase", "Matrix", "biomaRt", "cellHTS2", "doParallel", "dplyr", "foreach", "ggplot2", "glmnet", "reshape2"], 16457 "broken": true 16458 }, 16459 "girafe": { 16460 "name": "girafe", 16461 "version": "1.60.0", 16462 "sha256": "06cfbmr8y8xi3z3dl92w0ljl6w4px2m9nr28yp71i9yswa39j107", 16463 "depends": ["Biobase", "BiocGenerics", "Biostrings", "IRanges", "Rsamtools", "S4Vectors", "ShortRead", "genomeIntervals", "intervals", "pwalign"], 16464 "broken": true 16465 }, 16466 "gpart": { 16467 "name": "gpart", 16468 "version": "1.13.0", 16469 "sha256": "1518wjkaw22ckgpwl6si83bhijvib0r0kgs9s4das41f0ygi92sd", 16470 "depends": ["AnnotationDbi", "biomaRt", "data_table", "GenomicRanges", "Homo_sapiens", "igraph", "IRanges", "OrganismDbi", "Rcpp", "TxDb_Hsapiens_UCSC_hg38_knownGene"], 16471 "broken": true 16472 }, 16473 "gprege": { 16474 "name": "gprege", 16475 "version": "1.14.0", 16476 "sha256": "0mc8x8faj8pf8zb3mywjscn2rzs7bc0ws507a32r7zl5j8p9rzag", 16477 "depends": [], 16478 "broken": true 16479 }, 16480 "gpuMagic": { 16481 "name": "gpuMagic", 16482 "version": "1.23.0", 16483 "sha256": "0skgw46i3419i1bsinhkl12f1jv5gf2bxjr7j7ml5g7azypq61ha", 16484 "depends": ["BiocGenerics", "Deriv", "DescTools", "Rcpp", "digest", "pryr", "stringr"], 16485 "broken": true 16486 }, 16487 "granulator": { 16488 "name": "granulator", 16489 "version": "1.16.0", 16490 "sha256": "0ycwj878nyf8vc131781abvpz5dmyhdprflidw6gz5ywz16l7538", 16491 "depends": ["MASS", "cowplot", "dplyr", "dtangle", "e1071", "epiR", "ggplot2", "ggplotify", "limSolve", "magrittr", "nnls", "pheatmap", "purrr", "rlang", "tibble", "tidyr"], 16492 "broken": true 16493 }, 16494 "hca": { 16495 "name": "hca", 16496 "version": "1.16.0", 16497 "sha256": "1b2fj61m9h3h8ccly4y1ishr3ivrszpwc5j8rkkxy43nwmmv1r2p", 16498 "depends": ["BiocFileCache", "DT", "digest", "dplyr", "httr", "jsonlite", "miniUI", "readr", "shiny", "tibble", "tidyr"], 16499 "broken": true 16500 }, 16501 "hiAnnotator": { 16502 "name": "hiAnnotator", 16503 "version": "1.42.0", 16504 "sha256": "17c6v1w4lqiafvyfswf1p2wijzihawgazflwcviiq7dvx5qb0k6z", 16505 "depends": ["BSgenome", "GenomicRanges", "dplyr", "foreach", "ggplot2", "iterators", "rtracklayer", "scales"], 16506 "broken": true 16507 }, 16508 "hiReadsProcessor": { 16509 "name": "hiReadsProcessor", 16510 "version": "1.44.0", 16511 "sha256": "0xql5p20cqhwb5j13l643lshhrns45n4hg15x8lbk24r2zmb8azi", 16512 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomicAlignments", "GenomicRanges", "dplyr", "hiAnnotator", "pwalign", "readxl", "sonicLength"], 16513 "broken": true 16514 }, 16515 "hipathia": { 16516 "name": "hipathia", 16517 "version": "3.8.0", 16518 "sha256": "0lplbzcxgb1x5y5rqxr2jbl3a5fg7xh26p2i96mx39mmz8xvwnz0", 16519 "depends": ["AnnotationHub", "DelayedArray", "MetBrewer", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "coin", "dplyr", "ggplot2", "ggpubr", "igraph", "limma", "matrixStats", "preprocessCore", "reshape2", "servr", "tibble", "visNetwork"], 16520 "broken": true 16521 }, 16522 "htSeqTools": { 16523 "name": "htSeqTools", 16524 "version": "1.16.0", 16525 "sha256": "1bjbagx6s66fiia71n7ljg5rfc2v22bbp2sk718mf1i9i38c58lm", 16526 "depends": ["BSgenome", "Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "MASS"], 16527 "broken": true 16528 }, 16529 "hypeR": { 16530 "name": "hypeR", 16531 "version": "2.5.0", 16532 "sha256": "1c4ag9k8f91xyz3b57qrykj8kn467fh31lh41xw7vh1w7kwb0vjb", 16533 "depends": ["BiocStyle", "R6", "dplyr", "ggforce", "ggplot2", "htmltools", "httr", "igraph", "kableExtra", "magrittr", "msigdbr", "openxlsx", "purrr", "reactable", "reshape2", "rlang", "rmarkdown", "scales", "shiny", "stringr", "visNetwork"], 16534 "broken": true 16535 }, 16536 "iNETgrate": { 16537 "name": "iNETgrate", 16538 "version": "1.6.0", 16539 "sha256": "02862s4wqzmxhyvbk7d854wlp0whsww7g2w2ngwr5s4n1ri190p0", 16540 "depends": ["BiocStyle", "GenomicRanges", "Homo_sapiens", "Pigengene", "Rfast", "SummarizedExperiment", "WGCNA", "caret", "glmnet", "gplots", "igraph", "matrixStats", "minfi", "survival", "tidyr", "tidyselect"], 16541 "broken": true 16542 }, 16543 "iPAC": { 16544 "name": "iPAC", 16545 "version": "1.14.0", 16546 "sha256": "1gzxv6jkn7crylklmnvhm86gczmsr80dmw1a7flaisiiy40k128g", 16547 "depends": ["Biostrings", "gdata", "multtest", "scatterplot3d"], 16548 "broken": true 16549 }, 16550 "iPath": { 16551 "name": "iPath", 16552 "version": "1.14.0", 16553 "sha256": "0in8gcs669kcp397z5jishf26prgp86f7w86jwbdmi5j232xb9da", 16554 "depends": ["BiocParallel", "Rcpp", "RcppArmadillo", "ggplot2", "ggpubr", "matrixStats", "mclust", "survival", "survminer"], 16555 "broken": true 16556 }, 16557 "imageHTS": { 16558 "name": "imageHTS", 16559 "version": "1.20.0", 16560 "sha256": "1dg8cmrnzlv2qm5lf9771fiir5l0cql6pmfmv0l3037wisdgz1jw", 16561 "depends": ["Biobase", "EBImage", "cellHTS2", "e1071", "hwriter", "vsn"], 16562 "broken": true 16563 }, 16564 "inSilicoDb": { 16565 "name": "inSilicoDb", 16566 "version": "2.6.0", 16567 "sha256": "1avxm8qm9rblck94v0aq0na70jfl2cyr9xmbbk27n5hgp1cnaizf", 16568 "depends": ["Biobase", "RCurl", "rjson"], 16569 "broken": true 16570 }, 16571 "inSilicoMerging": { 16572 "name": "inSilicoMerging", 16573 "version": "1.14.0", 16574 "sha256": "1xiq66b0vjrcxf4nbmk5mmn1dlxbpa879z04f00w3yz1k7rx6782", 16575 "depends": ["Biobase"], 16576 "broken": true 16577 }, 16578 "inveRsion": { 16579 "name": "inveRsion", 16580 "version": "1.18.0", 16581 "sha256": "05jwxwjyvkilfmygf16k3d55ma7s1ya7lyxh8v4pd8gql7v3kllq", 16582 "depends": ["haplo_stats"], 16583 "broken": true 16584 }, 16585 "iontree": { 16586 "name": "iontree", 16587 "version": "1.16.0", 16588 "sha256": "1pamgkg85qi3iqqws7a3l8lph428alz1dzf08x309njqz8cbzw91", 16589 "depends": ["RSQLite", "XML", "rJava"], 16590 "broken": true 16591 }, 16592 "isomiRs": { 16593 "name": "isomiRs", 16594 "version": "1.36.1", 16595 "sha256": "1bcp2d2bc7fglq1kscxz8mdia6g8p80r3syvfrs42rql76hdvlfi", 16596 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "DEGreport", "DESeq2", "GGally", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "SummarizedExperiment", "broom", "cluster", "cowplot", "dplyr", "ggplot2", "gplots", "gridExtra", "gtools", "limma", "readr", "reshape", "rlang", "stringr", "tibble", "tidyr"], 16597 "broken": true 16598 }, 16599 "iterClust": { 16600 "name": "iterClust", 16601 "version": "1.24.0", 16602 "sha256": "0k2hcc7g4ynd9jrk8f286y6gwc4bfs4bnfs8qpj2i8zamwdaldng", 16603 "depends": ["Biobase", "cluster"], 16604 "broken": true 16605 }, 16606 "iteremoval": { 16607 "name": "iteremoval", 16608 "version": "1.15.1", 16609 "sha256": "0bwl8lzxvf5azwyacv9x16l4kyi8l00xny2s83gp2kng5gyz8602", 16610 "depends": ["GenomicRanges", "ggplot2", "magrittr", "SummarizedExperiment"], 16611 "broken": true 16612 }, 16613 "jmosaics": { 16614 "name": "jmosaics", 16615 "version": "1.10.0", 16616 "sha256": "1q67ylrgc2abny2wxgsl1cni225inar1dhim0psrbrf5ik77kgmk", 16617 "depends": ["mosaics"], 16618 "broken": true 16619 }, 16620 "joda": { 16621 "name": "joda", 16622 "version": "1.18.0", 16623 "sha256": "0fjbxczwkn8f4p0h8dgi3vfn4qf9a650wmp01q20j7f0jsmmb06x", 16624 "depends": ["RBGL", "bgmm"], 16625 "broken": true 16626 }, 16627 "lapmix": { 16628 "name": "lapmix", 16629 "version": "1.72.0", 16630 "sha256": "19bhb7654h8pivsf3qxv518zp02ijbvlhkb4d93nyanns3g7zqas", 16631 "depends": ["Biobase"], 16632 "broken": true 16633 }, 16634 "logitT": { 16635 "name": "logitT", 16636 "version": "1.28.0", 16637 "sha256": "1qbimjjl5xv5h30r74bd86dg10djajb01qav6gp95l6f59fx2j1q", 16638 "depends": ["affy"], 16639 "broken": true 16640 }, 16641 "lol": { 16642 "name": "lol", 16643 "version": "1.18.0", 16644 "sha256": "0dc3ga7yalzfngh3y33sa4bchhbxgndkls3vdxh4yzcsdvk60i1f", 16645 "depends": ["Matrix", "penalized"], 16646 "broken": true 16647 }, 16648 "lute": { 16649 "name": "lute", 16650 "version": "1.4.0", 16651 "sha256": "1f1i083aqhls9xf7hynb1xlk5r9ksm5jzy9l971ikh97jyxfwx22", 16652 "depends": ["Biobase", "BiocGenerics", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "dplyr", "ggplot2", "scran"], 16653 "broken": true 16654 }, 16655 "mAPKL": { 16656 "name": "mAPKL", 16657 "version": "1.2.0", 16658 "sha256": "1k1yxxj6371sagiy63fl1dh8d71cqg6gvx8pkjy3ahp1hbh45b6l", 16659 "depends": ["AnnotationDbi", "Biobase", "apcluster", "clusterSim", "e1071", "igraph", "limma", "multtest", "parmigene", "reactome_db"], 16660 "broken": true 16661 }, 16662 "mCSEA": { 16663 "name": "mCSEA", 16664 "version": "1.28.0", 16665 "sha256": "0j1yrdl9im2s8xfzb57km43v2613k8h6hq29ypxqm6g4x95nhpqf", 16666 "depends": ["GenomicFeatures", "GenomicRanges", "Gviz", "Homo_sapiens", "IRanges", "S4Vectors", "SummarizedExperiment", "biomaRt", "fgsea", "ggplot2", "limma", "mCSEAdata"], 16667 "broken": true 16668 }, 16669 "mQTL_NMR": { 16670 "name": "mQTL.NMR", 16671 "version": "1.4.0", 16672 "sha256": "0flb1lqsq7ldicidag20icnhmds2qr85yrbjsv4h06klggq2vjvg", 16673 "depends": ["MASS", "outliers", "qtl"], 16674 "broken": true 16675 }, 16676 "maanova": { 16677 "name": "maanova", 16678 "version": "1.40.0", 16679 "sha256": "112hbyfw18dshshsmbaylwra169w6bbwwqql3d96s0in1fl20mdl", 16680 "depends": ["Biobase"], 16681 "broken": true 16682 }, 16683 "macat": { 16684 "name": "macat", 16685 "version": "1.44.1", 16686 "sha256": "061y6a1q7c9r9a01hy6l86wc085f530y7hjw7asx506cf91ifwdk", 16687 "depends": ["Biobase", "annotate"], 16688 "broken": true 16689 }, 16690 "maigesPack": { 16691 "name": "maigesPack", 16692 "version": "1.34.0", 16693 "sha256": "08pszyq03f1vjgirq0zcv31m4c0acdbfh622qiw0x0w1gz6plm0g", 16694 "depends": ["convert", "graph", "limma", "marray"], 16695 "broken": true 16696 }, 16697 "manta": { 16698 "name": "manta", 16699 "version": "1.16.0", 16700 "sha256": "0j6zll7b1qqdnydg59hywargw6bivry3cx5m2wpj79wn673kib3c", 16701 "depends": ["Hmisc", "caroline", "edgeR"], 16702 "broken": true 16703 }, 16704 "mbOmic": { 16705 "name": "mbOmic", 16706 "version": "1.3.0", 16707 "sha256": "079qs5apyqli7h16c6drmhibmc356rnllxks5ddfnnq7hdzmhdbw", 16708 "depends": ["cluster", "clusterSim", "data_table", "doParallel", "igraph", "psych", "visNetwork", "WGCNA"], 16709 "broken": true 16710 }, 16711 "mcaGUI": { 16712 "name": "mcaGUI", 16713 "version": "1.18.0", 16714 "sha256": "0rxhs059z0l6lal33m78hkp73k46c2pdy0nn5lxwxr590fglvh0f", 16715 "depends": ["MASS", "OTUbase", "bpca", "foreign", "lattice", "proto", "vegan"], 16716 "broken": true 16717 }, 16718 "mdgsa": { 16719 "name": "mdgsa", 16720 "version": "1.2.0", 16721 "sha256": "05lqj7d4464z976w4rvnzpv1abihq1fpxhcl2zyg5izwqpq6ga9r", 16722 "depends": ["AnnotationDbi", "DBI", "GO_db", "KEGG_db", "Matrix", "cluster"], 16723 "broken": true 16724 }, 16725 "metaArray": { 16726 "name": "metaArray", 16727 "version": "1.48.0", 16728 "sha256": "1zx9ymjqh851r33jv7fpyy4319fqi2kgjgxxbgpq1xl6cfkglr4h", 16729 "depends": ["Biobase", "MergeMaid"], 16730 "broken": true 16731 }, 16732 "metaX": { 16733 "name": "metaX", 16734 "version": "1.0.3", 16735 "sha256": "1v4519spcgvc2kc1cah5gmfjnx09zlam8p8d8m6wkw0ba600vv7b", 16736 "depends": ["BBmisc", "CAMERA", "DiffCorr", "Nozzle_R1", "RColorBrewer", "RCurl", "SSPA", "VennDiagram", "ape", "boot", "bootstrap", "caret", "data_table", "doParallel", "dplyr", "faahKO", "ggplot2", "igraph", "impute", "lattice", "missForest", "pROC", "pcaMethods", "pheatmap", "pls", "plyr", "preprocessCore", "reshape2", "scatterplot3d", "stringr", "vsn", "xcms"], 16737 "broken": true 16738 }, 16739 "metabolomicsWorkbenchR": { 16740 "name": "metabolomicsWorkbenchR", 16741 "version": "1.18.0", 16742 "sha256": "1yk4ddcwqi72aq1jr7gj9c862g6fy82i0s7rx8a6y8nfigd1nvqd", 16743 "depends": ["MultiAssayExperiment", "SummarizedExperiment", "data_table", "httr", "jsonlite", "struct"], 16744 "broken": true 16745 }, 16746 "metagene": { 16747 "name": "metagene", 16748 "version": "2.2.1", 16749 "sha256": "1l0zfhk4gnm3gvy24igismpb3j3m6vh4mb4q41cfrpkmxn2zlvaq", 16750 "depends": ["BiocParallel", "DBChIP", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "IRanges", "R6", "Rsamtools", "ggplot2", "gplots", "rtracklayer"], 16751 "broken": true 16752 }, 16753 "metagenomeFeatures": { 16754 "name": "metagenomeFeatures", 16755 "version": "1.0.0", 16756 "sha256": "1lbb505s976j2jxxi7snhd1yahcs0ca9qnicq12b5jmp3ki1br9k", 16757 "depends": ["Biobase", "Biostrings", "RSQLite", "ShortRead", "dplyr", "lattice", "lazyeval", "magrittr", "stringr"], 16758 "broken": true 16759 }, 16760 "metaseqR": { 16761 "name": "metaseqR", 16762 "version": "1.10.0", 16763 "sha256": "1gy5ywrxqwd8lizbj9lk6qck6zwk670j5y2f0ayz6xvkki4vab97", 16764 "depends": ["DESeq", "EDASeq", "NBPSeq", "NOISeq", "baySeq", "biomaRt", "brew", "corrplot", "edgeR", "gplots", "limma", "log4r", "qvalue", "rjson", "vsn"], 16765 "broken": true 16766 }, 16767 "metavizr": { 16768 "name": "metavizr", 16769 "version": "1.21.0", 16770 "sha256": "1d88f854sn5m2pklsyvkmq05yzjanxlnkz5gpzban62qq1mpvims", 16771 "depends": ["Biobase", "data_table", "digest", "epivizr", "epivizrData", "epivizrServer", "epivizrStandalone", "GenomeInfoDb", "httr", "metagenomeSeq", "phyloseq", "vegan"], 16772 "broken": true 16773 }, 16774 "methVisual": { 16775 "name": "methVisual", 16776 "version": "1.22.0", 16777 "sha256": "1kcqhlv0lmr7wlkxjl9qqv2676pwna3i4w5xpm4inwgcb892zgjm", 16778 "depends": ["Biostrings", "IRanges", "ca", "gridBase", "gsubfn", "plotrix", "sqldf"], 16779 "broken": true 16780 }, 16781 "methyAnalysis": { 16782 "name": "methyAnalysis", 16783 "version": "1.12.2", 16784 "sha256": "0m4qx7q1zm3g4m8kwjz7nvf93891bmbvac0n8wpgniap669af0yk", 16785 "depends": ["AnnotationDbi", "Biobase", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "Gviz", "IRanges", "VariantAnnotation", "annotate", "biomaRt", "genefilter", "genoset", "lumi", "methylumi", "org_Hs_eg_db", "rtracklayer"], 16786 "broken": true 16787 }, 16788 "mfa": { 16789 "name": "mfa", 16790 "version": "1.30.0", 16791 "sha256": "0zgwf9sxgn0xb103f94zkd96264fjb7cshbwmbardlz74wvrjd87", 16792 "depends": ["Biobase", "MCMCglmm", "MCMCpack", "Rcpp", "coda", "dplyr", "ggmcmc", "ggplot2", "magrittr", "tibble"], 16793 "broken": true 16794 }, 16795 "miRmine": { 16796 "name": "miRmine", 16797 "version": "1.22.0", 16798 "sha256": "1d0ni3lavpiv2qzwlmrsjym75cip3i9q1bg9rwa04h61rz2smylg", 16799 "depends": ["SummarizedExperiment"], 16800 "broken": true 16801 }, 16802 "microSTASIS": { 16803 "name": "microSTASIS", 16804 "version": "1.8.0", 16805 "sha256": "1ixmd0srjndx43zsl183qzc1r4mhvm6cm2h5yshvijj4lhhgmfli", 16806 "depends": ["BiocParallel", "TreeSummarizedExperiment", "ggplot2", "ggside", "rlang", "stringr"], 16807 "broken": true 16808 }, 16809 "microbiomeMarker": { 16810 "name": "microbiomeMarker", 16811 "version": "1.12.2", 16812 "sha256": "0fkm2sqqsaa8kkdyp0j3zwx8lijgkgk4s45sir3s37an9yai2bp4", 16813 "depends": ["ALDEx2", "ANCOMBC", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "ComplexHeatmap", "DESeq2", "IRanges", "MASS", "S4Vectors", "biomformat", "caret", "coin", "dplyr", "edgeR", "ggplot2", "ggsignif", "ggtree", "limma", "magrittr", "metagenomeSeq", "multtest", "pROC", "patchwork", "phyloseq", "plotROC", "purrr", "rlang", "tibble", "tidyr", "tidytree", "vegan", "yaml"], 16814 "broken": true 16815 }, 16816 "mitoODE": { 16817 "name": "mitoODE", 16818 "version": "1.8.0", 16819 "sha256": "1rbxppzwmlrfyzcsa5b0biqm79qyv9662dh16zzp3frz56325kzy", 16820 "depends": ["KernSmooth", "MASS", "minpack_lm", "mitoODEdata"], 16821 "broken": true 16822 }, 16823 "mmnet": { 16824 "name": "mmnet", 16825 "version": "1.8.1", 16826 "sha256": "0ppcy11xnn593xig8gwz79vsbkdi3f5aai58zdhr59w52y2dafia", 16827 "depends": ["Biobase", "KEGGREST", "Matrix", "RCurl", "RJSONIO", "XML", "flexmix", "ggplot2", "igraph", "plyr", "reshape2", "stringr"], 16828 "broken": true 16829 }, 16830 "motifRG": { 16831 "name": "motifRG", 16832 "version": "1.14.0", 16833 "sha256": "1v9zm5629k2lcqbbgw8bwflvbircyxkfavbkvmbd212kgwcng8vn", 16834 "depends": ["BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "Biostrings", "IRanges", "XVector", "seqLogo"], 16835 "broken": true 16836 }, 16837 "multiOmicsViz": { 16838 "name": "multiOmicsViz", 16839 "version": "1.24.0", 16840 "sha256": "129k094ml403w25k3kipzbavx78p14jxq40a8d733qyqp8mcnlrs", 16841 "depends": ["doParallel", "foreach", "SummarizedExperiment"], 16842 "broken": true 16843 }, 16844 "multiSight": { 16845 "name": "multiSight", 16846 "version": "1.7.0", 16847 "sha256": "1v2ml1qh250lidm5a0xw4b3xbxd2as86p703qn5s8m1xi6l89b9c", 16848 "depends": ["anyLib", "biosigner", "caret", "clusterProfiler", "config", "DESeq2", "dplyr", "DT", "easyPubMed", "enrichplot", "ggnewscale", "golem", "htmltools", "igraph", "infotheo", "metap", "mixOmics", "networkD3", "ppcor", "R6", "ReactomePA", "rmarkdown", "rWikiPathways", "shiny", "shinydashboard", "stringr"], 16849 "broken": true 16850 }, 16851 "mvGST": { 16852 "name": "mvGST", 16853 "version": "1.4.0", 16854 "sha256": "1yi8558lkqfrmxgighb5v8q12gwqlbs2ds610fgf8ggrdn84bzq8", 16855 "depends": ["AnnotationDbi", "GO_db", "GOstats", "Rgraphviz", "annotate", "gProfileR", "graph", "stringr", "topGO"], 16856 "broken": true 16857 }, 16858 "nanotatoR": { 16859 "name": "nanotatoR", 16860 "version": "1.18.0", 16861 "sha256": "1nnh4g4b7k6mp922pr52sxlrh6wvfyx7jhckmwrd12l1yjq010pb", 16862 "depends": ["AnnotationDbi", "curl", "dplyr", "GenomicRanges", "hash", "httr", "knitr", "openxlsx", "org_Hs_eg_db", "rentrez", "rlang", "stringr", "testthat", "tidyverse", "XML"], 16863 "broken": true 16864 }, 16865 "neaGUI": { 16866 "name": "neaGUI", 16867 "version": "1.8.0", 16868 "sha256": "1xms5k8zzbk31sj0f92rsqjv40vcqy89pmy8z3j0336iascqbx9l", 16869 "depends": ["hwriter"], 16870 "broken": true 16871 }, 16872 "nem": { 16873 "name": "nem", 16874 "version": "2.44.0", 16875 "sha256": "1bkq622jyrfn0v4wyw5ycxmri8kyils4wznsz26ki3awff34lq3h", 16876 "depends": ["RBGL", "RColorBrewer", "Rgraphviz", "boot", "e1071", "graph", "limma", "plotrix", "statmod"], 16877 "broken": true 16878 }, 16879 "netDx": { 16880 "name": "netDx", 16881 "version": "1.16.0", 16882 "sha256": "00ghcj5hzb06pi9aj2rdnasyqgqnvr9qjb0m6b0476yv2mx5x24k", 16883 "depends": ["BiocFileCache", "GenomeInfoDb", "GenomicRanges", "IRanges", "MultiAssayExperiment", "RColorBrewer", "ROCR", "Rtsne", "S4Vectors", "bigmemory", "combinat", "doParallel", "foreach", "ggplot2", "glmnet", "httr", "igraph", "plotrix", "pracma", "rappdirs", "reshape2"], 16884 "broken": true 16885 }, 16886 "netOmics": { 16887 "name": "netOmics", 16888 "version": "1.8.0", 16889 "sha256": "03nyjvcr2hldsfifj0dix1bc79z05i9x2hgc5z2g9hd1jyijljyd", 16890 "depends": ["AnnotationDbi", "dplyr", "ggplot2", "GO_db", "gprofiler2", "igraph", "magrittr", "minet", "purrr", "RandomWalkRestartMH", "tibble", "tidyr"], 16891 "broken": true 16892 }, 16893 "netZooR": { 16894 "name": "netZooR", 16895 "version": "1.10.0", 16896 "sha256": "11rq1lhxhwij6wik087wmnzk8aswhmmf3yzcpiljxbk8szsm8np7", 16897 "depends": ["AnnotationDbi", "Biobase", "GO_db", "GOstats", "MASS", "Matrix", "RCy3", "STRINGdb", "assertthat", "data_table", "doParallel", "dplyr", "foreach", "ggdendro", "ggplot2", "gplots", "igraph", "matrixStats", "matrixcalc", "nnet", "org_Hs_eg_db", "pandaR", "penalized", "reshape", "reshape2", "reticulate", "tidyr", "vegan", "viridisLite", "yarn"], 16898 "broken": true 16899 }, 16900 "netbenchmark": { 16901 "name": "netbenchmark", 16902 "version": "1.2.0", 16903 "sha256": "10s8xsisjp9sj9dl67bgn94ipm6a6kpqli3pvjdpxkmvjkg400kg", 16904 "depends": ["GeneNet", "Matrix", "Rcpp", "c3net", "corpcor", "fdrtool", "grndata", "minet", "pracma", "randomForest"], 16905 "broken": true 16906 }, 16907 "netbiov": { 16908 "name": "netbiov", 16909 "version": "1.4.0", 16910 "sha256": "1h3986kfi516xlw675cq901ls9v7rj5rr0ls5lny21wd439n2avf", 16911 "depends": ["igraph"], 16912 "broken": true 16913 }, 16914 "netboxr": { 16915 "name": "netboxr", 16916 "version": "1.9.0", 16917 "sha256": "1brnm60745s2axls4p6qcxipjjr3ph9ijg1q604fgm42rf6i7qzm", 16918 "depends": ["clusterProfiler", "data_table", "DT", "gplots", "igraph", "jsonlite", "plyr", "RColorBrewer"], 16919 "broken": true 16920 }, 16921 "networkBMA": { 16922 "name": "networkBMA", 16923 "version": "1.12.0", 16924 "sha256": "0zkf10iqiabsln1jxq0sypr43mrw6k82l3pdp5bg9kcv0bqqqy5k", 16925 "depends": ["BMA", "Rcpp", "RcppArmadillo", "RcppEigen"], 16926 "broken": true 16927 }, 16928 "nudge": { 16929 "name": "nudge", 16930 "version": "1.36.0", 16931 "sha256": "1px6hnda7hp7yx9imkl8xq8m772csd2qic0kq5bqwshk5qdvfhw7", 16932 "depends": [], 16933 "broken": true 16934 }, 16935 "oneChannelGUI": { 16936 "name": "oneChannelGUI", 16937 "version": "1.36.0", 16938 "sha256": "0r5y531y4niy9gh64n7nk8a0xcj8lyg36axhcjx116ycsqa00x5h", 16939 "depends": ["Biobase", "Biostrings", "IRanges", "Rsamtools", "affylmGUI", "chimera", "siggenes", "tkWidgets", "tkrplot"], 16940 "broken": true 16941 }, 16942 "oneSENSE": { 16943 "name": "oneSENSE", 16944 "version": "1.20.0", 16945 "sha256": "1lzb8i3frv3va2q28glwnjwszrynhky5y8fx10q4h52p2wqgc4v3", 16946 "depends": ["flowCore", "gplots", "plotly", "Rtsne", "scatterplot3d", "shiny", "shinyFiles", "webshot"], 16947 "broken": true 16948 }, 16949 "ontoCAT": { 16950 "name": "ontoCAT", 16951 "version": "1.22.0", 16952 "sha256": "03vy4210m31jzhhhbhw3ixhm1lji4qil2zp0ckmyh3xb8m8s8fzl", 16953 "depends": ["rJava"], 16954 "broken": true 16955 }, 16956 "openPrimeRui": { 16957 "name": "openPrimeRui", 16958 "version": "1.26.0", 16959 "sha256": "0w00ya6xb70am000hybrxgcq8bpd950w36n01v4l0pfmfcvqd9fa", 16960 "depends": ["DT", "openPrimeR", "rmarkdown", "shiny", "shinyBS", "shinyjs"], 16961 "broken": true 16962 }, 16963 "oppti": { 16964 "name": "oppti", 16965 "version": "1.21.0", 16966 "sha256": "0v7hy9qy3mjx8sj3rvs23sy38r8nfgr4d4na4k8h65y2mi8xfqnp", 16967 "depends": ["RColorBrewer", "devtools", "ggplot2", "knitr", "limma", "parallelDist", "pheatmap", "reshape"], 16968 "broken": true 16969 }, 16970 "pareg": { 16971 "name": "pareg", 16972 "version": "1.8.0", 16973 "sha256": "1b9vvn1ppw1vbfmkzkbd6b01pkqnsknbrjv1js983dpjv23x6xlb", 16974 "depends": ["DOSE", "Matrix", "basilisk", "devtools", "doFuture", "doRNG", "dplyr", "foreach", "future", "ggplot2", "ggraph", "ggrepel", "glue", "hms", "igraph", "keras", "logger", "magrittr", "nloptr", "progress", "proxy", "purrr", "reticulate", "rlang", "stringr", "tensorflow", "tfprobability", "tibble", "tidygraph", "tidyr"], 16975 "broken": true 16976 }, 16977 "pathVar": { 16978 "name": "pathVar", 16979 "version": "1.0.1", 16980 "sha256": "1ixraifr8d86m9rdg38d6kfzmgghjxasgi3abb1i8knjyfwrc05v", 16981 "depends": ["EMT", "Matching", "data_table", "ggplot2", "gridExtra", "mclust"], 16982 "broken": true 16983 }, 16984 "paxtoolsr": { 16985 "name": "paxtoolsr", 16986 "version": "1.4.6", 16987 "sha256": "170gm5qxlsz2dv249q16shpj0xm9y7rp3rpn9ij6r2c5d3xn8i21", 16988 "depends": ["R_utils", "XML", "data_table", "httr", "igraph", "plyr", "rJava", "rjson"], 16989 "broken": true 16990 }, 16991 "pcaGoPromoter": { 16992 "name": "pcaGoPromoter", 16993 "version": "1.14.0", 16994 "sha256": "1w0cpakxlm8dx6z3j844xmkz3dawiaschrjcjlkqjv9ay8vfkhz8", 16995 "depends": ["AnnotationDbi", "Biostrings", "ellipse"], 16996 "broken": true 16997 }, 16998 "pcot2": { 16999 "name": "pcot2", 17000 "version": "1.38.0", 17001 "sha256": "1ycsbry5srf1msq4vcvv0q34lgzkwadh7k1pgwv963i567i4lx3b", 17002 "depends": ["Biobase", "amap"], 17003 "broken": true 17004 }, 17005 "pcxn": { 17006 "name": "pcxn", 17007 "version": "2.26.0", 17008 "sha256": "13gahdsvz7ss3chcvqmdyrnw31rcgiplqg7awrn930drwljlimqk", 17009 "depends": ["pcxnData", "pheatmap"], 17010 "broken": true 17011 }, 17012 "pdmclass": { 17013 "name": "pdmclass", 17014 "version": "1.42.0", 17015 "sha256": "1f4zrxbyk49hm0cxp0g1786cwc7g1k5z6v3hn2z66m7rbapz8afy", 17016 "depends": ["Biobase", "fibroEset", "mda"], 17017 "broken": true 17018 }, 17019 "perturbatr": { 17020 "name": "perturbatr", 17021 "version": "1.13.0", 17022 "sha256": "0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31", 17023 "depends": ["assertthat", "diffusr", "doParallel", "dplyr", "foreach", "formula_tools", "ggplot2", "igraph", "lazyeval", "lme4", "magrittr", "rlang", "scales", "tibble", "tidyr"], 17024 "broken": true 17025 }, 17026 "phemd": { 17027 "name": "phemd", 17028 "version": "1.18.0", 17029 "sha256": "174jp26insq2mwf9yw9bls4i9b2a8vccfkrg2h1dzvyyk513bi83", 17030 "depends": ["Biobase", "BiocGenerics", "cluster", "cowplot", "destiny", "ggplot2", "igraph", "maptree", "monocle", "phateR", "pheatmap", "pracma", "RANN", "RColorBrewer", "reticulate", "Rtsne", "S4Vectors", "scatterplot3d", "Seurat", "SingleCellExperiment", "SummarizedExperiment", "transport", "VGAM"], 17031 "broken": true 17032 }, 17033 "phenoDist": { 17034 "name": "phenoDist", 17035 "version": "1.18.0", 17036 "sha256": "0kjsdgvr5kmrnn7mjzphk5r6irgjv5cfgmrd4yddprbmmln39avn", 17037 "depends": ["e1071", "imageHTS"], 17038 "broken": true 17039 }, 17040 "pint": { 17041 "name": "pint", 17042 "version": "1.20.0", 17043 "sha256": "19q21b3zdn4adx49zn88z69xz3mqza58xdhig3zicn9s0g21bfz4", 17044 "depends": ["Matrix", "mvtnorm"], 17045 "broken": true 17046 }, 17047 "pkgDepTools": { 17048 "name": "pkgDepTools", 17049 "version": "1.36.0", 17050 "sha256": "1v2fsax49wklwdmgxp9pjyp18cbj2rsg7yd68mwr2amlihgvmsp1", 17051 "depends": ["RBGL", "graph"], 17052 "broken": true 17053 }, 17054 "plateCore": { 17055 "name": "plateCore", 17056 "version": "1.28.0", 17057 "sha256": "1v7shvjnav930grswbixj8fyabmamsgry5g5is3sf9ymp9r8gh5x", 17058 "depends": ["Biobase", "MASS", "flowCore", "flowStats", "flowViz", "lattice", "latticeExtra", "robustbase"], 17059 "broken": true 17060 }, 17061 "plethy": { 17062 "name": "plethy", 17063 "version": "1.8.0", 17064 "sha256": "1skaqws1yb8n8li4daprq4x8vrbyykm3fk6pzwx7iyr3nf2r2zz5", 17065 "depends": ["Biobase", "BiocGenerics", "DBI", "IRanges", "RColorBrewer", "RSQLite", "S4Vectors", "Streamer", "ggplot2", "plyr", "reshape2"], 17066 "broken": true 17067 }, 17068 "plrs": { 17069 "name": "plrs", 17070 "version": "1.10.0", 17071 "sha256": "1f2dlgcbpfrn5za2z7nf1y8jzrcb5hzb3gix18nyqmz9syg57zha", 17072 "depends": ["Biobase", "BiocGenerics", "CGHbase", "Rcsdp", "ic_infer", "marray", "quadprog"], 17073 "broken": true 17074 }, 17075 "plw": { 17076 "name": "plw", 17077 "version": "1.30.0", 17078 "sha256": "190bccvxhdgp3ah9vzdpjddb33ck38r5x4gw1f8vwxh0mw79vf9c", 17079 "depends": ["MASS", "affy"], 17080 "broken": true 17081 }, 17082 "polyester": { 17083 "name": "polyester", 17084 "version": "1.6.0", 17085 "sha256": "0if2rbgbfc3ghz5mnmpmpv6rq63qjm3l16gmlr493vfrpxdzclnv", 17086 "depends": ["Biostrings", "IRanges", "S4Vectors", "limma", "logspline"], 17087 "broken": true 17088 }, 17089 "ppiStats": { 17090 "name": "ppiStats", 17091 "version": "1.36.0", 17092 "sha256": "1s5xv565w924g71qaxgmhfszrkqs3arzi8l0vzcz446r2pgm6d32", 17093 "depends": ["Biobase", "Category", "RColorBrewer", "ScISI", "graph", "lattice", "ppiData"], 17094 "broken": true 17095 }, 17096 "prada": { 17097 "name": "prada", 17098 "version": "1.46.0", 17099 "sha256": "0ak21586bbkbpwji1pcbr44dlwyhslscrqm2y172310xbxm0sqbg", 17100 "depends": ["Biobase", "BiocGenerics", "MASS", "RColorBrewer", "rrcov"], 17101 "broken": true 17102 }, 17103 "predictionet": { 17104 "name": "predictionet", 17105 "version": "1.16.0", 17106 "sha256": "1q7nl11kvh2rl5rzb4qnq5ckdrdkna0arfnjmki35lr8hyh65id0", 17107 "depends": ["MASS", "RBGL", "igraph", "penalized"], 17108 "broken": true 17109 }, 17110 "proBatch": { 17111 "name": "proBatch", 17112 "version": "1.14.0", 17113 "sha256": "079dh61v1dmsasrh5sn6sn1rgi34mavxa1sc1y8x6wqjwabm4w1j", 17114 "depends": ["Biobase", "corrplot", "data_table", "dplyr", "ggfortify", "ggplot2", "lazyeval", "lubridate", "magrittr", "pheatmap", "preprocessCore", "purrr", "pvca", "RColorBrewer", "reshape2", "rlang", "scales", "sva", "tibble", "tidyr", "viridis", "wesanderson", "WGCNA"], 17115 "broken": true 17116 }, 17117 "proFIA": { 17118 "name": "proFIA", 17119 "version": "1.23.0", 17120 "sha256": "0y08vj401f45dvgxjwjx94hvd0rk1wljk8n1irpkdafg24gv4fvj", 17121 "depends": ["Biobase", "BiocParallel", "minpack_lm", "missForest", "pracma", "ropls", "xcms"], 17122 "broken": true 17123 }, 17124 "profileplyr": { 17125 "name": "profileplyr", 17126 "version": "1.24.1", 17127 "sha256": "02y423r6g9bi7g5izvrwmxmrxrkyah8496pdrm1xhq97i9k8pdba", 17128 "depends": ["BiocGenerics", "BiocParallel", "ChIPseeker", "ComplexHeatmap", "EnrichedHeatmap", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "IRanges", "R_utils", "Rsamtools", "S4Vectors", "SummarizedExperiment", "TxDb_Hsapiens_UCSC_hg19_knownGene", "TxDb_Hsapiens_UCSC_hg38_knownGene", "TxDb_Mmusculus_UCSC_mm10_knownGene", "TxDb_Mmusculus_UCSC_mm9_knownGene", "circlize", "dplyr", "ggplot2", "magrittr", "org_Hs_eg_db", "org_Mm_eg_db", "pheatmap", "rGREAT", "rjson", "rlang", "rtracklayer", "soGGi", "tidyr", "tiff"], 17129 "broken": true 17130 }, 17131 "prot2D": { 17132 "name": "prot2D", 17133 "version": "1.8.0", 17134 "sha256": "0pmsl550wvxnqx5zbj8b6lhvlb2bcmvi3xxx66x8r1sz3cdy3l7h", 17135 "depends": ["Biobase", "MASS", "Mulcom", "fdrtool", "impute", "limma", "qvalue", "samr", "st"], 17136 "broken": true 17137 }, 17138 "proteasy": { 17139 "name": "proteasy", 17140 "version": "1.2.0", 17141 "sha256": "1mfk69k44krdj4wp6xpil391j9jrppyx1crvra525p8hahzc2d5m", 17142 "depends": ["AnnotationFilter", "data_table", "EnsDb_Hsapiens_v86", "EnsDb_Mmusculus_v79", "EnsDb_Rnorvegicus_v79", "ensembldb", "Rcpi", "stringr"], 17143 "broken": true 17144 }, 17145 "proteoQC": { 17146 "name": "proteoQC", 17147 "version": "1.6.0", 17148 "sha256": "15raykmw19k4yn4jppw4lqwgarr8b7sfsvhcif49xvw7k1dwj5ys", 17149 "depends": ["MSnbase", "Nozzle_R1", "Rcpp", "VennDiagram", "XML", "ggplot2", "plyr", "rTANDEM", "reshape2", "seqinr"], 17150 "broken": true 17151 }, 17152 "psygenet2r": { 17153 "name": "psygenet2r", 17154 "version": "1.36.0", 17155 "sha256": "1khjid5lkkn5qpnk9adw1in4km41q067mj5r5yqs2iz5hv4vx6xv", 17156 "depends": ["BgeeDB", "Biobase", "GO_db", "RCurl", "biomaRt", "ggplot2", "igraph", "labeling", "reshape2", "stringr", "topGO"], 17157 "broken": true 17158 }, 17159 "pulsedSilac": { 17160 "name": "pulsedSilac", 17161 "version": "1.9.1", 17162 "sha256": "1zb8xzs9h4rcrnmsfvrwb1qixn3jbnzxdwqgdrb82hgmxabmajlb", 17163 "depends": ["cowplot", "ggplot2", "ggridges", "MuMIn", "R_utils", "robustbase", "S4Vectors", "SummarizedExperiment", "UpSetR"], 17164 "broken": true 17165 }, 17166 "pwOmics": { 17167 "name": "pwOmics", 17168 "version": "1.2.0", 17169 "sha256": "0vlr71mhch716xl2i0366pxjkawci0g2imvfhsqinv5gd92m6hpq", 17170 "depends": ["AnnotationDbi", "AnnotationHub", "Biobase", "BiocGenerics", "GenomicRanges", "STRINGdb", "biomaRt", "data_table", "gplots", "igraph", "rBiopaxParser"], 17171 "broken": true 17172 }, 17173 "pwrEWAS": { 17174 "name": "pwrEWAS", 17175 "version": "1.14.0", 17176 "sha256": "1913h2syad9mfspxjvmrwm0mrcklbcl89lj04rn5x0xgfk8rk58a", 17177 "depends": ["abind", "BiocManager", "CpGassoc", "doParallel", "doSNOW", "foreach", "genefilter", "ggplot2", "limma", "pwrEWAS_data", "shiny", "shinyBS", "shinyWidgets", "truncnorm"], 17178 "broken": true 17179 }, 17180 "qckitfastq": { 17181 "name": "qckitfastq", 17182 "version": "1.24.0", 17183 "sha256": "16lcg42jclw24nk1k9bxy7vm3qj5vyqny99b0ixm0ilda6wkl1f7", 17184 "depends": ["RSeqAn", "Rcpp", "data_table", "dplyr", "ggplot2", "magrittr", "reshape2", "rlang", "seqTools", "zlibbioc"], 17185 "broken": true 17186 }, 17187 "qrqc": { 17188 "name": "qrqc", 17189 "version": "1.24.0", 17190 "sha256": "0850frx6fg9py2laav0yqavl9ckbn6y475xm9r6gxvyzp63smzdg", 17191 "depends": ["Biostrings", "Rsamtools", "biovizBase", "brew", "ggplot2", "plyr", "reshape", "testthat", "xtable"], 17192 "broken": true 17193 }, 17194 "rDGIdb": { 17195 "name": "rDGIdb", 17196 "version": "1.30.0", 17197 "sha256": "1v96nj1ffmg1678p7rspcqsnqvwcssv96jcyqqbb8v8sryflwmi5", 17198 "depends": ["httr", "jsonlite"], 17199 "broken": true 17200 }, 17201 "rGADEM": { 17202 "name": "rGADEM", 17203 "version": "2.55.0", 17204 "sha256": "1fjqvkayam7xpvvbdlz6nafgsrw46vgmbkl96mfvm4szclrxzs8g", 17205 "depends": ["BSgenome", "Biostrings", "GenomicRanges", "IRanges", "seqLogo"], 17206 "broken": true 17207 }, 17208 "rHVDM": { 17209 "name": "rHVDM", 17210 "version": "1.36.0", 17211 "sha256": "0k1gccnac59q54y2nypzgip2srs5yg3v2hhrz86ps50p2lx4pqd2", 17212 "depends": ["Biobase", "R2HTML", "affy", "minpack_lm"], 17213 "broken": true 17214 }, 17215 "rMAT": { 17216 "name": "rMAT", 17217 "version": "3.20.0", 17218 "sha256": "0dq4ipz1j6qai8q8z038hjb5j0w67gp7449vj8psgca2854gxa7s", 17219 "depends": ["Biobase", "BiocGenerics", "IRanges", "affxparser"], 17220 "broken": true 17221 }, 17222 "rSFFreader": { 17223 "name": "rSFFreader", 17224 "version": "0.18.0", 17225 "sha256": "0z2lkjbs3svx1b9zr4smjwrcd9xzxhfp98428vzaqq0k79h1v666", 17226 "depends": ["Biostrings", "IRanges", "S4Vectors", "ShortRead", "XVector"], 17227 "broken": true 17228 }, 17229 "rTANDEM": { 17230 "name": "rTANDEM", 17231 "version": "1.10.0", 17232 "sha256": "1dmaqdjfmjkkrddf666hpp95s7s6x0ssinx9aybl6952ylfjgcd1", 17233 "depends": ["Rcpp", "XML", "data_table"], 17234 "broken": true 17235 }, 17236 "rama": { 17237 "name": "rama", 17238 "version": "1.44.0", 17239 "sha256": "0nka6a2dk7jn4lk0i2p91hxwdgpny6y3j4dz709crrxlz3xjqflm", 17240 "depends": [], 17241 "broken": true 17242 }, 17243 "reb": { 17244 "name": "reb", 17245 "version": "1.48.0", 17246 "sha256": "1bxijf91vdr6088459r29kvy691bjbscy170pc0739iqbg7z80zm", 17247 "depends": ["Biobase", "idiogram"], 17248 "broken": true 17249 }, 17250 "receptLoss": { 17251 "name": "receptLoss", 17252 "version": "1.20.0", 17253 "sha256": "1b6lfs7dmizyvl1x21rf2h07pc04x7ains30zn64p8xrg6cxkfr9", 17254 "depends": ["SummarizedExperiment", "dplyr", "ggplot2", "magrittr", "tidyr"], 17255 "broken": true 17256 }, 17257 "regionalpcs": { 17258 "name": "regionalpcs", 17259 "version": "1.6.0", 17260 "sha256": "07c66bi8df6pl6biim16z108mv5zb5cr7xzifm41vbfj2cwyjkdp", 17261 "depends": ["GenomicRanges", "PCAtools", "dplyr", "tibble"], 17262 "broken": true 17263 }, 17264 "restfulSE": { 17265 "name": "restfulSE", 17266 "version": "1.24.0", 17267 "sha256": "0i40yfvynxy34jfkvzyvjwvxf89zi4pvy9m9i0bk93l17gyhnjyl", 17268 "depends": ["AnnotationDbi", "AnnotationHub", "bigrquery", "Biobase", "DBI", "DelayedArray", "dplyr", "ExperimentHub", "GO_db", "magrittr", "reshape2", "rhdf5client", "rlang", "S4Vectors", "SummarizedExperiment"], 17269 "broken": true 17270 }, 17271 "rnaSeqMap": { 17272 "name": "rnaSeqMap", 17273 "version": "2.28.0", 17274 "sha256": "0mfcy7l31g5z5yv12sv9imaf19p9vawnk7cqcm50x2sm032r8n7f", 17275 "depends": ["Biobase", "DBI", "DESeq", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "edgeR"], 17276 "broken": true 17277 }, 17278 "rols": { 17279 "name": "rols", 17280 "version": "3.4.0", 17281 "sha256": "1v6sp43j9ls4mxmfhzr3slq9kbhsnhwk7400i832yk1p7i0l9h4v", 17282 "depends": ["Biobase", "BiocGenerics", "httr2", "jsonlite"], 17283 "broken": true 17284 }, 17285 "sRAP": { 17286 "name": "sRAP", 17287 "version": "1.10.0", 17288 "sha256": "080s88l3a2fbgqnc8sy41kwzkm6skjazkirqini7n6xqcsqb9lih", 17289 "depends": ["ROCR", "WriteXLS", "gplots", "pls", "qvalue"], 17290 "broken": true 17291 }, 17292 "sampleClassifier": { 17293 "name": "sampleClassifier", 17294 "version": "1.32.0", 17295 "sha256": "18cmgpwwd54mkkpg13wjznbk71lp0bz1p5ics9mhxiq6vfw8i62l", 17296 "depends": ["MGFM", "MGFR", "annotate", "e1071", "ggplot2"], 17297 "broken": true 17298 }, 17299 "sapFinder": { 17300 "name": "sapFinder", 17301 "version": "1.8.0", 17302 "sha256": "12a0wcjxcz77b06bymhqcj5wxzm478mlj9vcvbbqhdfvj7214hy9", 17303 "depends": ["Rcpp", "pheatmap", "rTANDEM"], 17304 "broken": true 17305 }, 17306 "saps": { 17307 "name": "saps", 17308 "version": "2.2.0", 17309 "sha256": "11v7nxlcnkslxl0giv3y2naxpfsmqmrj6b4y2g6zbp48zml45jgl", 17310 "depends": ["piano", "reshape2", "survcomp", "survival"], 17311 "broken": true 17312 }, 17313 "savR": { 17314 "name": "savR", 17315 "version": "1.8.0", 17316 "sha256": "1vxxmzr8k6fn9fqr0pbfvccqq30d8w3fwjcr5x0bh1d77mzgf9n1", 17317 "depends": ["XML", "ggplot2", "gridExtra", "reshape2", "scales"], 17318 "broken": true 17319 }, 17320 "sbgr": { 17321 "name": "sbgr", 17322 "version": "1.0.0", 17323 "sha256": "0bvvxd0c4k4mmwkcb9w02i2kb6vwlq84w8vfqiamnwjy2vgjgka9", 17324 "depends": ["httr", "jsonlite", "objectProperties"], 17325 "broken": true 17326 }, 17327 "scAlign": { 17328 "name": "scAlign", 17329 "version": "1.12.0", 17330 "sha256": "1mlhxwsfrmhysa5mcyx7vf2jn49snf41yb7xqmyi40wilj9h8qlb", 17331 "depends": ["FNN", "ggplot2", "irlba", "purrr", "Rtsne", "Seurat", "SingleCellExperiment", "tensorflow"], 17332 "broken": true 17333 }, 17334 "scClassifR": { 17335 "name": "scClassifR", 17336 "version": "1.2.0", 17337 "sha256": "0p9l9q5ina0axrqvqn1y5wkfqi0nacxm3nm6ny34j53znv07b2zz", 17338 "depends": ["ape", "caret", "data_tree", "dplyr", "e1071", "ggplot2", "kernlab", "pROC", "ROCR", "Seurat", "SingleCellExperiment", "SummarizedExperiment"], 17339 "broken": true 17340 }, 17341 "scFeatures": { 17342 "name": "scFeatures", 17343 "version": "1.8.0", 17344 "sha256": "0srvd9jayyy3793jmm7pcq70m4mhvdc9qhsszbnnl2qcd33wsnkv", 17345 "depends": ["AUCell", "BiocParallel", "DT", "DelayedArray", "DelayedMatrixStats", "EnsDb_Hsapiens_v79", "EnsDb_Mmusculus_v79", "GSVA", "MatrixGenerics", "Seurat", "SingleCellSignalR", "ape", "cli", "dplyr", "ensembldb", "glue", "gtools", "msigdbr", "proxyC", "reshape2", "rmarkdown", "spatstat_explore", "spatstat_geom", "tidyr"], 17346 "broken": true 17347 }, 17348 "scMAGeCK": { 17349 "name": "scMAGeCK", 17350 "version": "1.9.1", 17351 "sha256": "1i6l8jxrd66aqk3m9212wsi8jqklvs0agsqrllvf9mrh16js4vby", 17352 "depends": ["ggplot2", "Seurat"], 17353 "broken": true 17354 }, 17355 "scQTLtools": { 17356 "name": "scQTLtools", 17357 "version": "1.0.3", 17358 "sha256": "0k1ps1l56a7ybk28py515c39a9b798ysh7c47zj3w6fqncc6gpl7", 17359 "depends": ["DESeq2", "GOSemSim", "Matrix", "SeuratObject", "SingleCellExperiment", "SummarizedExperiment", "VGAM", "biomaRt", "dplyr", "gamlss", "ggplot2", "limma", "magrittr", "patchwork", "progress", "stringr"], 17360 "broken": true 17361 }, 17362 "scsR": { 17363 "name": "scsR", 17364 "version": "1.6.0", 17365 "sha256": "0g1vgx8wrdwbhlzmf0a11fg5jnbkvz402h8qj48vj4bq8j202bc1", 17366 "depends": ["BiocGenerics", "Biostrings", "IRanges", "RColorBrewer", "STRINGdb", "ggplot2", "hash", "plyr", "sqldf"], 17367 "broken": true 17368 }, 17369 "seq2pathway": { 17370 "name": "seq2pathway", 17371 "version": "1.40.0", 17372 "sha256": "1js23facw3z31fn4g8xrnxsvwfj4ij1spancl243wwnpdspw2vwy", 17373 "depends": ["GSA", "GenomicRanges", "WGCNA", "biomaRt", "nnet", "seq2pathway_data"], 17374 "broken": true 17375 }, 17376 "seqArchR": { 17377 "name": "seqArchR", 17378 "version": "1.12.0", 17379 "sha256": "05i8ln6dbq46v4gnajmrfrnsi2y7mw22dzsmcbc6zni64c2r0186", 17380 "depends": ["BiocParallel", "Biostrings", "MASS", "Matrix", "cli", "cluster", "cvTools", "fpc", "ggplot2", "ggseqlogo", "matrixStats", "prettyunits", "reshape2", "reticulate"], 17381 "broken": true 17382 }, 17383 "seqArchRplus": { 17384 "name": "seqArchRplus", 17385 "version": "1.8.0", 17386 "sha256": "17pby4jz6422ndfkxzq19r7js01ai2mp4m6jn1dj622a16gvgkp4", 17387 "depends": ["BSgenome", "BiocParallel", "Biostrings", "ChIPseeker", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "S4Vectors", "cli", "clusterProfiler", "cowplot", "factoextra", "ggimage", "ggplot2", "gridExtra", "heatmaps", "magick", "scales", "seqArchR", "seqPattern"], 17388 "broken": true 17389 }, 17390 "seqCNA": { 17391 "name": "seqCNA", 17392 "version": "1.16.0", 17393 "sha256": "1wq92wszv0x99l52lm3k0zc2ffin1sp78xlyfabxpwi1v0yrkifl", 17394 "depends": ["GLAD", "adehabitatLT", "doSNOW", "seqCNA_annot"], 17395 "broken": true 17396 }, 17397 "seqTools": { 17398 "name": "seqTools", 17399 "version": "1.42.0", 17400 "sha256": "0g9308wmrz9mkf8r1vg8pbz7z2bpcqd6invn30aka18r8kwcim7s", 17401 "depends": ["zlibbioc"], 17402 "broken": true 17403 }, 17404 "seqbias": { 17405 "name": "seqbias", 17406 "version": "1.18.0", 17407 "sha256": "1wwskcbl3wd8gl63jl4wl0xwzj8kbwbc8xhp12z3xximngkk7dgd", 17408 "depends": ["Biostrings", "GenomicRanges", "Rsamtools", "zlibbioc"], 17409 "broken": true 17410 }, 17411 "seqplots": { 17412 "name": "seqplots", 17413 "version": "1.8.1", 17414 "sha256": "0anv2048m5zp2ijfzk79avcwzp662gw0y58j7nafha21j5s2qyhm", 17415 "depends": ["BSgenome", "Biostrings", "DBI", "DT", "GenomeInfoDb", "GenomicRanges", "IRanges", "RColorBrewer", "RSQLite", "S4Vectors", "class", "digest", "fields", "ggplot2", "gridExtra", "jsonlite", "kohonen", "plotrix", "reshape2", "rtracklayer", "shiny"], 17416 "broken": true 17417 }, 17418 "shiny_gosling": { 17419 "name": "shiny.gosling", 17420 "version": "1.4.0", 17421 "sha256": "1as7hrs3kfwxlr9zykdm88gv985gdnmzlrb2hn9zcgsalika53in", 17422 "depends": ["digest", "fs", "htmltools", "jsonlite", "rjson", "rlang", "shiny", "shiny_react"], 17423 "broken": true 17424 }, 17425 "shinyTANDEM": { 17426 "name": "shinyTANDEM", 17427 "version": "1.8.0", 17428 "sha256": "0dkgwfynznpq2q55d83w4x0nmal3dkgzxi1jpdcsasqlhsyqvmvx", 17429 "depends": ["mixtools", "rTANDEM", "shiny", "xtable"], 17430 "broken": true 17431 }, 17432 "sigPathway": { 17433 "name": "sigPathway", 17434 "version": "1.38.0", 17435 "sha256": "126cyw88d6rxp3bzdqsmm2v0kvhn650qmi4zcs9v50n0hhwyrxrf", 17436 "depends": [], 17437 "broken": true 17438 }, 17439 "sigaR": { 17440 "name": "sigaR", 17441 "version": "1.14.0", 17442 "sha256": "07ip468liyg9b6q9izd1wdp29p9f2icfs01nf0il4gc76h6d0rr5", 17443 "depends": ["Biobase", "CGHbase", "MASS", "corpcor", "igraph", "marray", "mvtnorm", "penalized", "quadprog", "snowfall"], 17444 "broken": true 17445 }, 17446 "simpleaffy": { 17447 "name": "simpleaffy", 17448 "version": "2.46.0", 17449 "sha256": "1x3f7hm7w44yarq4irv791330zfamhsqqwnqz8xfwrpvjrkv6avn", 17450 "depends": ["Biobase", "BiocGenerics", "affy", "gcrma", "genefilter"], 17451 "broken": true 17452 }, 17453 "simulatorZ": { 17454 "name": "simulatorZ", 17455 "version": "1.4.0", 17456 "sha256": "1sypvrwq6ay7lzmb9cmpix1zgzafzryvf4my5jky846bcpam91qj", 17457 "depends": ["Biobase", "BiocGenerics", "GenomicRanges", "Hmisc", "IRanges", "S4Vectors", "SummarizedExperiment", "gbm", "survival"], 17458 "broken": true 17459 }, 17460 "single": { 17461 "name": "single", 17462 "version": "1.7.0", 17463 "sha256": "0h7h9m4xr65nayr707jvjnbic1q4z0hsghw5i3pfpz2n6p9pb8s8", 17464 "depends": ["BiocGenerics", "Biostrings", "GenomicAlignments", "IRanges", "Rsamtools", "dplyr", "reshape2", "rlang", "stringr", "tidyr"], 17465 "broken": true 17466 }, 17467 "slinky": { 17468 "name": "slinky", 17469 "version": "1.12.0", 17470 "sha256": "05ywydvyz3jnzbhabhz1sd61hpy9nb22512zpbi48mv5wic1sv3v", 17471 "depends": ["curl", "dplyr", "foreach", "httr", "jsonlite", "readr", "rhdf5", "SummarizedExperiment", "tidyr"], 17472 "broken": true 17473 }, 17474 "snapCGH": { 17475 "name": "snapCGH", 17476 "version": "1.40.0", 17477 "sha256": "0fjqp0qhwk041pgwqp3av5ihkf4xb9li6zy6gmvk24hlj8sm600z", 17478 "depends": ["DNAcopy", "GLAD", "aCGH", "cluster", "limma", "tilingArray"], 17479 "broken": true 17480 }, 17481 "soGGi": { 17482 "name": "soGGi", 17483 "version": "1.40.1", 17484 "sha256": "0qz7ilxxp8f9yi2bhp7w6nk8jrakmp8ymi0r7zqzmr2ldjp03ans", 17485 "depends": ["BiocGenerics", "BiocParallel", "Biostrings", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors", "SummarizedExperiment", "chipseq", "ggplot2", "preprocessCore", "reshape2", "rtracklayer"], 17486 "broken": true 17487 }, 17488 "sojourner": { 17489 "name": "sojourner", 17490 "version": "1.11.0", 17491 "sha256": "1s0iqzn65s9g4yymy059z122i9wvgkcb5718snzxhj7mkqjzwhhc", 17492 "depends": ["dplyr", "EBImage", "fitdistrplus", "ggplot2", "gridExtra", "lattice", "MASS", "mclust", "minpack_lm", "mixtools", "mltools", "nls2", "pixmap", "plyr", "R_matlab", "Rcpp", "reshape2", "rlang", "scales", "shiny", "shinyjs", "sp", "truncnorm"], 17493 "broken": true 17494 }, 17495 "spade": { 17496 "name": "spade", 17497 "version": "1.18.2", 17498 "sha256": "0m2784x2ysp4mc7m8n8scpr1h38m3p9glcc5jd6cix55bh3yzykk", 17499 "depends": ["Biobase", "flowCore", "igraph"], 17500 "broken": true 17501 }, 17502 "sparseDOSSA": { 17503 "name": "sparseDOSSA", 17504 "version": "1.24.0", 17505 "sha256": "1xy9kd5a9vilwkgr4xw6lcdwgwykg7q7kildpfw4gqymd1frnjp6", 17506 "depends": ["MASS", "MCMCpack", "optparse", "tmvtnorm"], 17507 "broken": true 17508 }, 17509 "spatialHeatmap": { 17510 "name": "spatialHeatmap", 17511 "version": "2.14.1", 17512 "sha256": "002w2srp628asbwjc5q8jn51f4czrbna8raqa0sb1w7qlhckccak", 17513 "depends": ["Matrix", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "data_table", "dplyr", "edgeR", "genefilter", "ggplot2", "ggplotify", "grImport", "gridExtra", "igraph", "reshape2", "rsvg", "shiny", "shinydashboard", "spsComps", "tibble", "xml2"], 17514 "broken": true 17515 }, 17516 "spatzie": { 17517 "name": "spatzie", 17518 "version": "1.14.0", 17519 "sha256": "1jvz4szaqx1l7n87dd68mzpgpskxarpkg36qz0nx9x0d9xv4a9jd", 17520 "depends": ["BSgenome", "BiocGenerics", "GenomeInfoDb", "GenomicFeatures", "GenomicInteractions", "GenomicRanges", "IRanges", "MatrixGenerics", "S4Vectors", "SummarizedExperiment", "TFBSTools", "ggplot2", "matrixStats", "motifmatchr"], 17521 "broken": true 17522 }, 17523 "spliceR": { 17524 "name": "spliceR", 17525 "version": "1.12.0", 17526 "sha256": "0r5j0ibl2ccsxb7rr2fxw4b07wbdiyfndxkl4pgd9h0ks4qyhyjy", 17527 "depends": ["GenomicRanges", "IRanges", "RColorBrewer", "VennDiagram", "cummeRbund", "plyr", "rtracklayer"], 17528 "broken": true 17529 }, 17530 "spliceSites": { 17531 "name": "spliceSites", 17532 "version": "1.8.3", 17533 "sha256": "1jifh0nbqjhrc07jfc50hfk4wn1hv3a863rbr3fnqlg9rwg044w7", 17534 "depends": ["Biobase", "BiocGenerics", "Biostrings", "IRanges", "doBy", "seqLogo"], 17535 "broken": true 17536 }, 17537 "splicegear": { 17538 "name": "splicegear", 17539 "version": "1.42.0", 17540 "sha256": "1g2fqql1wqzwz1vx5cq03ckld0gccqk6rv9l99xsaa8mhf0rn1qa", 17541 "depends": ["Biobase", "XML", "annotate"], 17542 "broken": true 17543 }, 17544 "spotSegmentation": { 17545 "name": "spotSegmentation", 17546 "version": "1.44.0", 17547 "sha256": "074nzh18pj6dpk9bqh8id0j2vpaxvhi2ddrz6hnza381wzdgxdr3", 17548 "depends": ["mclust"], 17549 "broken": true 17550 }, 17551 "sscore": { 17552 "name": "sscore", 17553 "version": "1.42.0", 17554 "sha256": "0h86crb241vmaczp76wz4zv9ni1snmlkrdi1md3hgq1hqxnn9gzs", 17555 "depends": ["affy", "affyio"], 17556 "broken": true 17557 }, 17558 "staRank": { 17559 "name": "staRank", 17560 "version": "1.12.0", 17561 "sha256": "1vgc3mhxyhrgwkapnqx4061l9l0nyc012508hma14xbxml3f76sg", 17562 "depends": ["cellHTS2"], 17563 "broken": true 17564 }, 17565 "stepwiseCM": { 17566 "name": "stepwiseCM", 17567 "version": "1.16.0", 17568 "sha256": "1ss79yr75kw7fsd8ihpivj9k5v32zxr3ymkl6prba0nyxdj5wyz9", 17569 "depends": ["Biobase", "e1071", "glmpath", "pamr", "penalized", "randomForest", "snowfall", "tspair"], 17570 "broken": true 17571 }, 17572 "struct": { 17573 "name": "struct", 17574 "version": "1.20.2", 17575 "sha256": "0280k9mv8q46fh78yhr5hxp5xayszl0q8qn39xhndin7i50pwni3", 17576 "depends": ["S4Vectors", "SummarizedExperiment", "knitr", "ontologyIndex", "rols"], 17577 "broken": true 17578 }, 17579 "structToolbox": { 17580 "name": "structToolbox", 17581 "version": "1.20.0", 17582 "sha256": "1wy0bw3a6q11w1fi4i17kswfjql9865rim1znhrmfq91vqndqldp", 17583 "depends": ["ggplot2", "ggthemes", "gridExtra", "scales", "sp", "struct"], 17584 "broken": true 17585 }, 17586 "supraHex": { 17587 "name": "supraHex", 17588 "version": "1.8.0", 17589 "sha256": "1g2zcarzi805y2933pyjdgg7l9imbhdf4pjhyr8bir0149li98cy", 17590 "depends": ["MASS", "ape", "hexbin"], 17591 "broken": true 17592 }, 17593 "synapter": { 17594 "name": "synapter", 17595 "version": "2.31.0", 17596 "sha256": "09jcnaw6mhcwk1mzysk3ryy6j11dasj3dkz7gajlgm855wcznkmp", 17597 "depends": ["Biobase", "Biostrings", "MSnbase", "RColorBrewer", "cleaver", "lattice", "multtest", "qvalue", "readr", "rmarkdown"], 17598 "broken": true 17599 }, 17600 "tidytof": { 17601 "name": "tidytof", 17602 "version": "1.2.0", 17603 "sha256": "13m028bm21j7404ncvpg7l7qvfkbvcnbrf4rp3xilyl5m6cyvidy", 17604 "depends": ["Rcpp", "RcppHNSW", "doParallel", "dplyr", "flowCore", "foreach", "ggplot2", "ggraph", "glmnet", "purrr", "readr", "recipes", "rlang", "stringr", "survival", "tibble", "tidygraph", "tidyr", "tidyselect", "yardstick"], 17605 "broken": true 17606 }, 17607 "tofsims": { 17608 "name": "tofsims", 17609 "version": "1.22.0", 17610 "sha256": "0da4843wbcr821yp8z3z4vd81qpm2lblckgd01fm89lmwj393z65", 17611 "depends": ["ALS", "alsace", "KernSmooth", "ProtGenerics", "Rcpp", "RcppArmadillo", "signal"], 17612 "broken": true 17613 }, 17614 "traviz": { 17615 "name": "traviz", 17616 "version": "1.10.0", 17617 "sha256": "1jjdfl8xvzlr31w74j12s5pdg5b1yylg1i30n804p9mqyx11g5sc", 17618 "depends": ["Biobase", "RColorBrewer", "SingleCellExperiment", "SummarizedExperiment", "ggplot2", "mgcv", "princurve", "rgl", "slingshot", "viridis"], 17619 "broken": true 17620 }, 17621 "trena": { 17622 "name": "trena", 17623 "version": "1.22.2", 17624 "sha256": "1xjhqm2g53kgcnnqhs5l3vn525h7amaz4hvsskjp5zb0gkfpiwh1", 17625 "depends": ["AnnotationDbi", "biomaRt", "Biostrings", "BSgenome", "BSgenome_Hsapiens_UCSC_hg19", "BSgenome_Hsapiens_UCSC_hg38", "BSgenome_Mmusculus_UCSC_mm10", "DBI", "GenomicRanges", "glmnet", "lassopv", "MotifDb", "org_Hs_eg_db", "randomForest", "RMySQL", "RPostgreSQL", "RSQLite", "SNPlocs_Hsapiens_dbSNP150_GRCh38", "WGCNA", "xgboost"], 17626 "broken": true 17627 }, 17628 "triform": { 17629 "name": "triform", 17630 "version": "1.12.0", 17631 "sha256": "0pqfz6msalr2264iwi2hzam2sv8yl4fy1ri72pff5gh14rbxgiml", 17632 "depends": ["BiocGenerics", "IRanges", "yaml"], 17633 "broken": true 17634 }, 17635 "trigger": { 17636 "name": "trigger", 17637 "version": "1.53.0", 17638 "sha256": "1m1gwqjz8b72csygl0yp2jz3i9pv8yxgb3gk5s53bbh27wfh9hk8", 17639 "depends": ["corpcor", "qtl", "qvalue", "sva"], 17640 "broken": true 17641 }, 17642 "tscR": { 17643 "name": "tscR", 17644 "version": "1.11.0", 17645 "sha256": "19jpmyb6dly7l0418c1z0dlb936wjh6nwkb0mvk13ym19qgv1my7", 17646 "depends": ["class", "cluster", "dplyr", "dtw", "GenomicRanges", "ggplot2", "gridExtra", "IRanges", "knitr", "latex2exp", "prettydoc", "RColorBrewer", "rmarkdown", "S4Vectors", "SummarizedExperiment"], 17647 "broken": true 17648 }, 17649 "tspair": { 17650 "name": "tspair", 17651 "version": "1.28.0", 17652 "sha256": "0m083g5z77n7dd4lnbhvbwjkykh7a4pl4v8j7ipr5w7f9dhdjk33", 17653 "depends": ["Biobase"], 17654 "broken": true 17655 }, 17656 "waveTiling": { 17657 "name": "waveTiling", 17658 "version": "1.12.0", 17659 "sha256": "0j866mgxj44mv4wp0yqnav83w8pfb47lmjhp1y0qqvxc6q9k80g8", 17660 "depends": ["Biobase", "Biostrings", "GenomeGraphs", "GenomicRanges", "IRanges", "affy", "oligo", "oligoClasses", "preprocessCore", "waveslim"], 17661 "broken": true 17662 }, 17663 "wppi": { 17664 "name": "wppi", 17665 "version": "1.16.0", 17666 "sha256": "17rkfbhy0r22ayca4c7n8gr2kjgbj3r4gk1rh423cp566x0n7pcp", 17667 "depends": ["Matrix", "OmnipathR", "RCurl", "dplyr", "igraph", "logger", "magrittr", "progress", "purrr", "rlang", "tibble", "tidyr"], 17668 "broken": true 17669 }, 17670 "xps": { 17671 "name": "xps", 17672 "version": "1.30.0", 17673 "sha256": "0wh98fsj3j368bxk4wa7rjd3acwl04r1dfiy13a89zv1fzv3wvky", 17674 "depends": [], 17675 "broken": true 17676 }, 17677 "yaqcaffy": { 17678 "name": "yaqcaffy", 17679 "version": "1.30.0", 17680 "sha256": "1pj2ksqbj7dlc76s6qagi7iq35wa83gx5cp0hm42w3bj7mxprjbi", 17681 "depends": ["simpleaffy"], 17682 "broken": true 17683 }, 17684 "zlibbioc": { 17685 "name": "zlibbioc", 17686 "version": "1.54.0", 17687 "sha256": "0ll3v5b9yk63rqiwm4g0dwan22mqkj2lv1b6czwghbpl1jpv2jrd", 17688 "depends": [], 17689 "broken": true 17690 } 17691 } 17692}