Question: Suggestions for R/Bioconductor packages for GSE analysis
0
gravatar for kieran-lievel
5 months ago by
kieran-lievel0 wrote:

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

Thanks, Kieran

R • 203 views
ADD COMMENTlink modified 5 months ago by ATpoint21k • written 5 months ago by kieran-lievel0

Thanks a lot! Very helpful

ADD REPLYlink written 5 months ago by kieran-lievel0
2
gravatar for benformatics
5 months ago by
benformatics1.1k
ETH Zurich
benformatics1.1k wrote:

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.

ADD COMMENTlink written 5 months ago by benformatics1.1k

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

ADD REPLYlink written 6 days ago by Papyrus10
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