scPS

(single-cell Pathway Score)

scPS is a single-cell RNA-seq gene set analysis (scGSA) method using the functions in R script (without installation)

Input Data:

1. A Seurat object (Seurat V5 are required),

2. A gene matrix transposed (GMT) file format of gene sets/pathways. Each gene set is described by a name, a description, and the genes in the gene set.

Output:

1. Single cells with corresponding scores for gene sets/pathways data matrix, where rows correspond to gene sets/pathways and columns correspond to cells.

How to Apply scPS Function

Seurat_data = Input Seurat object

GeneSet = Gene set gmt file

Result = scPS(Seurat_data,GeneSet) # calling scPS

libraries required

library(Seurat) #Seurat V5 library(GSEABase) library(genefilter)

All the raw data for the data simulation and comparative analysis can be found at the following link: https://drive.google.com/drive/folders/1Gvp4ydnJbHZEDIxLjyt0xrQcbMziwDBF?usp=drive_link

Authors:Ruoqiao Wang and Juilee Thakar

Email:RuoQiao_Wang@URMC.Rochester.edu and juilee_thakar@urmc.rochester.edu