Question: gene set enrichment analysis
0
gravatar for Bogdan
13 months ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 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 • 276 views
ADD COMMENTlink modified 13 months ago by Gordon Smyth39k • written 13 months ago by Bogdan580
Answer: gene set enrichment analysis
0
gravatar for Gordon Smyth
13 months ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k 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 13 months ago • written 13 months ago by Gordon Smyth39k

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 13 months ago • written 13 months ago by Bogdan580
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 250 users visited in the last hour