Hello all,

I have a large bulk RNA seq set of DEGs and I am looking to try to do GSEA using my own curated gene list from Single Cell RNA seq published data. I want to know the enrichment of these single cell lists in my list of ranked DEGs.

My question is, most GSEA vignettes and tutorials use msigDB or other linked databases and I can't figure out how to tailor the code using my own GMT file.

Any help would be great!

Hi,

you can import the contents of a GMT file using the function getGmt() from the GSEABase package.

cheers,

robert.