byarielm.fyi
sc-ImmuCC: Hierarchical annotation for immune cell types in single-cell RNA-Seq#
Installation#
R programming language >= 4.1.1 ，packages Seurat and GSVA are required to use scImmuCC.
The installation from GitHub is in experimental stage but it can be used normally when the dependencies are installed:
if (!requireNamespace("Seurat", quietly = TRUE))
install.packages("Seurat")
if (!requireNamespace("GSVA", quietly = TRUE))
BiocManager::install("GSVA")
if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("wuaipinglab/scImmuCC")
Example#
Below is an example 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)
QuickStart#
The following is a quick tutorial on how to use scImmuCC to annotate immune cell types in scRNA-Seq.
library(scImmuCC)
count <- read.csv(file=filename) ##read your scRNA-Seq file
count <- as.matrix(count) ## a matrix with cell unique barcodes as column names and gene names as row names
test <- scImmuCC_Layered(test_data,Non_Immune=FALSE) ##if your data have non-immune cell, Non_Immune = TRUE