runGO: Calculating pathway enrichment scores for scATAC-seq profiles
In reggenlab/UniPath: UniPath provides robust statistical methods to represent every single cell using pathway and gene-set enrichment scores. It can be used with both single cell RNA-seq and single cell ATAC-seq profile with scalability for atlas scale data-sets. Unipath comes with several features like psuedo-temporal ordering using pathway scores and unconventional way of enumerating differences between two cell populations.

Calculating pathway enrichment scores for scATAC-seq profiles

1 2	runGO(gmtFile, BGfile, countFile, method, globalaccessibility_scores, FGfile, promoters = FALSE)

`gmtFile`	gene-set file
`BGfile`	background file
`countFile`	scATAC-seq count matrix
`method`	If method is chosen as 1, data normalization is performed using global accessibility scores. If selected method is 2 then local accessibility score-based normalization is performed
`globalaccessibility_scores`	global accessibility scores for input count data matrix
`FGfile`	foreground file
`promoters`	whether promoters to be used or not for conversion of scATAC-seq profiles to pathway scores. Default is false