byarielm.fyi / scImmuCC
Hierarchical annotation of immune cells in scRNA-Seq data based on ssGSEA algorithm. Fork for large datasets with QOL improvements.
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sc-ImmuCC: Hierarchical annotation for immune cell types in single-cell RNA-Seq#

The below demonstrates the result of Hierarchical annotation for some immune cells in the E-MTAB-11536 dataset (included in the package)

library(scImmuCC)

data(package="scImmuCC) data(test_data,package="scImmuCC") # load the test data

count <- as.matrix(test_data) # Convert test data to matrix

test <- scImmuCC_Layered(count = count ,Non_Immune = FALSE)

#In