README.md

In dongzhuoer/qGSEA: Simplest tool to prepare GSEA input files

qGSEA

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.

dongzhuoer/qGSEA documentation built on Aug. 8, 2020, 9:40 a.m.