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