Dear all,
we wish you a fruitful autumn time ! I would like to ask for a piece of advice, particularly, which R/BioC package would you recommend for GSEA (and it is close to java implementation available at http://software.broadinstitute.org/gsea/doc/desktop_tutorial.jsp ).
many thanks for your suggestions,
-- bogdan
I am assuming that you want, not just gene set enrichment analysis in general, but the specific GSEA method published by the Broad Institute. As far I know, there is no public R package that is equivalent to the Broad Institute's Java "GSEA" method. This discussion on Biostars is relevant: https://www.biostars.org/p/96332/
I note that you asked the same question on this forum a few years ago, but without the reference to the Broad Institute's Java implementation: gene set (enrichment) analysis
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version 2.3.6
Dear Gordon, thank you for your message.
Yes, I have used a while ago the java implementation of GSEA that is available from Broad Institute, together with MSigDB database. Now, I am re-writing some RNA-seq analysis pipeline in R, and ideally, I would like to have all the analysis "chapters" in R, that I could run in a very automated way.
I've just came across EnrichmentBrowser package
(https://bioconductor.org/packages/release/bioc/vignettes/EnrichmentBrowser/inst/doc/EnrichmentBrowser.pdf),
and now I am checking whether the script :
provides a good alternative. I can see that we could use as method also "roast", and "camera". Thank you ..