Overview

GSEA is a powerful tool, but preparing its input files, escpecially from GSE raw data, is a painful process. I know that from very personal experience, that’s why I develop thistool. You just need a GSE accession and qGSEA would take care of everything else for you.

Installation

if (!('devtools' %in% .packages(T))) install.packages('devtools')
remotes::install_github('dongzhuoer/qGSEA')

Usage

refer to vignette('qGSEA').

Tips

For using GSEA in non-human organisms, you can find gene sets here (.gmt files ready for downloading).

Especially, for mouse, you shouldn’t miss the Bioconductor package gskb, it collect gene sets from various sources.