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GSEA - Software or R

I have been reading about GSEA and functional enrichment, and I am confused about how to do GSEA. I know that there is a software, but R packages like clusterProfiler and gprofiler2 also let us do the GSEA analysis. So, what is the difference between these and how do we decide if we want to do the enrichment on the software or on R?

Thanks!

enrichment rna-seq r gsea functional
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written by estafana.t98 • estafana.t98

To be clear, there are two different classes of enrichment test that are in frequent use. These are Over-representation analysis (ORA) and functional class scoring (FCS). GSEA is the stereotypical FCS software, while clusterProfiler and gprofiler2 are best known for ORA tests. I see that clusterprofiler now supports an FCS test which is great (link).

One thing that should be noted is that these enrichment tests make the statistical assumption that genes measurements are independent, whereas in fact they are mostly correlated.

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written by mark.ziemann mark.ziemann

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