ScPAS
A tool for identifying Phenotype-Associated cell Subpopulations from single-cell sequencing data by integrating bulk data
Install / Use
/learn @aiminXie/ScPASREADME
scPAS : Single-Cell Phenotype-Associated Subpopulation identifier
A tool for identifying phenotype-associated cell subpopulations from single-cell sequencing data by integrating bulk data
Introduction
scPAS is a new tool which enables the quantitative estimation of the strength of association between each cell in scRNA-seq data and a phenotype by constructing a network-regularized sparse regression model. This model integrates bulk RNA-seq data with phenotype information and the gene-gene similarity network from single-cell data.
The workflow of scPAS is shown in the following Figure:
<p align="center"> <img src=Flow_diagram.png height="492" width="700"> </p>Installation
- System requirements: scPAS is developed under R (version >= 4.0.5).
- scPAS R package can be installed from Github using devtools:
devtools::install_github("aiminXie/scPAS").
Installation of other dependencies if not automatically installed
- Install Seurat using
install.packages('Seurat'). - Install Rcpp using
install.packages('Rcpp'). - Install Matrix using
install.packages('Matrix'). - Install preprocessCore using
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install( "preprocessCore").
Tutorial
How to cite scPAS
Please cite the following manuscript:
Xie A, Wang H, Zhao J, Wang Z, Xu J, Xu Y. (2024) scPAS: single-cell phenotype-associated subpopulation identifier. Brief Bioinform 26(1):bbae655. https://doi.org/10.1093/bib/bbae655.
