Cell Set Overlap Analysis (CSOA) is a tool for calculating per-cell gene signature scores in an scRNA-seq dataset. CSOA constructs a set for each gene in the signature, consisting of the cells that highly express the gene. Next, all overlaps of pairs of cell sets are computed, ranked, filtered and scored. The CSOA per-cell score is calculated by summing up all products of the overlap scores and the min-max-normalized expression of the two involved genes.

To install CSOA, run the following R code:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    
BiocManager::install("CSOA")

The basic command to run CSOA is:

runCSOA(scObj, geneSets)

scObj must contain normalized and log-transformed gene expression data provided in one of the following formats:

• Seurat.
  • CSOA will use the expression matrix stored in the data layer.
• SingleCellExperiment
  • CSOA will use the expression matrix stored in the logcounts assay.
• matrix
• dgCMatrix

geneSets must be a named list of character vectors.