# scPS (Single-Cell Pathway Score) scPS is a single-cell RNA-seq gene set analysis (scGSA) method designed to evaluate gene set activity at the single-cell level. It utilizes functions within an R script, eliminating the need for additional installation. The tool integrates seamlessly with Seurat V5 objects for efficient pathway scoring across thousands of cells.

✨ Features

Input:
•	A Seurat object (Seurat V5 is required)
•	A gene set file in GMT (Gene Matrix Transposed) format. This file should contain gene set names, descriptions, and the associated genes.
Output:
•	A matrix where rows correspond to gene sets/pathways and columns correspond to single cells, with each cell assigned a score for each gene set or pathway.

🛠️ How to Use scPS

Seurat_data = Input Seurat object  
GeneSet = Gene set gmt file  
Result = scPS(Seurat_data, GeneSet)  #Calling scPS  

📚 Required Libraries

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

🔗 Data Availability

The raw data for simulation and comparative analysis are available here

👩‍🔬 Authors

Ruoqiao Wang (Email: RuoQiao_Wang@URMC.Rochester.edu)

📄 Citation

✨ Please cite when using scPS ✨

Wang, R. H., & Thakar, J. (2024). Comparative analysis of single-cell pathway scoring methods and a novel approach. NAR Genomics and Bioinformatics, 6(3), lqae124