Suggestions for R/Bioconductor packages for GSE analysis

Question

[kieran-lievel]

Hi everyone, which are the most used R / Bioconductor packages to perform a gene set enrichment analysis?

Thanks, Kieran

[kieran-lievel]

Thanks a lot! Very helpful

Answer 1

[benformatics]

Based on the 100 most downloaded Bioconductor pacakges:

fgsea

clusterProfiler

Category

topGO

GOstats

The Broad also has their own R script/package I think: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/R-GSEA_Readme

Feel free to correct me if I missed some.

[Papyrus]

I would certainly add the limma package, which contains functionality for several gene set enrichment tests (roast, camera, romer). And also goseq, to perform the simpler over-representation analyses