Question: gene set enrichment analysis
0
gravatar for Bogdan
8 months ago by
Bogdan550
Palo Alto, CA, USA
Bogdan550 wrote:

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

gsea gsa • 221 views
ADD COMMENTlink modified 8 months ago by Gordon Smyth37k • written 8 months ago by Bogdan550
Answer: gene set enrichment analysis
0
gravatar for Gordon Smyth
8 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

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

ADD COMMENTlink modified 8 months ago • written 8 months ago by Gordon Smyth37k

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 :

sbea(method="gsea", se=allSE, gs=hsa.gs, perm=0, alpha=0.1)

provides a good alternative. I can see that we could use as method also "roast", and "camera". Thank you ..

 

 

ADD REPLYlink modified 8 months ago • written 8 months ago by Bogdan550
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