cal_PAS: calculation Pathway Activity Score
In zgyaru/testSctpa: A portable toolkit for pathway activity score calculation

parameters 'counts', 'gSets_path' and 'gSets' are consistent across all tools

cal_PAS(
  seurat_object,
  tool = c("AUCell", "Vision", "GSVA", "ssGSEA", "plage", "zscore"),
  species = "none",
  pathway = "none",
  gmt_file = "none",
  normalize = "sctransform",
  n_cores = 3,
  rand_seed = 123
)

`tool`	tool name
`species`	species; human or mouse
`pathway`	abbreviation for pathway database
`gmt_file`	pathways in GMT format
`normalize`	normalization method
`counts`	gene expresion matrix, rows are genes and cols are cells
`filter`	whether filtering for genes expressed in less than 5 percent cells