enrichIt: Calculate gene set enrichment scores for single-cell data
In escape: Easy single cell analysis platform for enrichment

Description Usage Arguments Value Author(s) See Also Examples

This function allows users to input both the single-cell RNA-sequencing counts and any gene set pathways either from the stored data or from other sources. The enrichment calculation itself uses the gsva R package and the poisson distribution for RNA.

1	enrichIt(obj, gene.sets = NULL, groups = 1000, cores = 2)

`obj`	The count matrix, Seurat, or SingleCellExperiment object.
`gene.sets`	Gene sets from `getGeneSets` to use for the enrichment analysis.
`groups`	The number of cells to separate the enrichment calculation.
`cores`	The number of cores to use for parallelization.

Data frame of normalized enrichmenet scores (NES)

Nick Borcherding, Jared Andrews

getGeneSets to collect gene sets.

GS <- getGeneSets(library = "H")
GS <- GS[[1]] #Reduce list size for example
seurat_ex <- suppressWarnings(Seurat::pbmc_small)
ES <- enrichIt(obj = seurat_ex, gene.sets = GS)