Question: Gene set enrichment analysis
1
gravatar for Bogdan
5 months ago by
Bogdan720
Palo Alto, CA, USA
Bogdan720 wrote:

Dear all,

we wish you a fruitful autumn time ! I would like to ask for a piece of advice, particularly, which package would you recommend for GSEA (preferably in R/BioC, and it is close to java implementation available at http://software.broadinstitute.org/gsea/doc/desktop_tutorial.jsp ).

many thanks for your suggestions,

-- bogdan

R gsea gsa enrichment • 434 views
ADD COMMENTlink modified 5 months ago by zx87546.8k • written 5 months ago by Bogdan720
1

Have you tried WebGestalt or its R implementation, WebGestaltR? We have a new version with a much more intuitive UI!

ADD REPLYlink written 5 months ago by RamRS20k

Thank you very much for your suggestions.

I have been looking into WebGestaltR documentation (https://cran.r-project.org/web/packages/WebGestaltR/WebGestaltR.pdf), and if I may ask, what is the simplest setup of the command "WebGestaltR" ?

In the package manual, it is written :

WebGestaltR(enrichMethod="ORA", organism="hsapiens",
    enrichDatabase="geneontology_Biological_Process",enrichDatabaseFile=NULL,
    enrichDatabaseType=NULL,enrichDatabaseDescriptionFile=NULL,interestGeneFile=NULL,
    interestGene=NULL,interestGeneType=NULL,collapseMethod="mean",referenceGeneFile=NULL,
    referenceGene=NULL,referenceGeneType=NULL,referenceSet=NULL, minNum=10, maxNum=500,
    fdrMethod="BH",sigMethod="fdr",fdrThr=0.05,topThr=10,dNum=20,perNum=1000,
    lNum=20,is.output=TRUE,outputDirectory=getwd(),projectName=NULL,keepGSEAFolder=FALSE,
    methodType="R",dagColor="binary",hostName="http://www.webgestalt.org/")
ADD REPLYlink modified 5 months ago by RamRS20k • written 5 months ago by Bogdan720

All the parameters with recommended values have them as default values. You can check out the Webgestalt user forum here. I'm sorry, I'm not too familiar with WebgestaltR.

ADD REPLYlink modified 5 months ago • written 5 months ago by RamRS20k

Thanks a lot, Ram !

yes, we would like to include Webgestalt (preferably WebgestaltR) in our R computational pipeline.

ADD REPLYlink written 5 months ago by Bogdan720
1

Hi Bogdan,

We just recently implemented GSEA and it is still in development branch. You can check it out at here. It is designed to add weights to each "gene" in the "gene set", but can also perform standard GSEA as well. I just added a utility function to help load and format the input. It is pure R now and feels like a little bit slower than original.

If you just need to run GSEA with your own data, I think you can take the GSEA file alone for now. We are going to merge dev into master branch and release a new version on CRAN later this year.

(The beta version of WebGestalt already uses the new version in the backend. One of the benefit is that we can get leading edge genes and make GSEA enrichment plot for all the gene sets, not limited by -plot_top_x parameter, for example.)

ADD REPLYlink modified 5 months ago • written 5 months ago by Trypto10
0
gravatar for Malcolm.Cook
5 months ago by
Malcolm.Cook1.0k
kansas, usa
Malcolm.Cook1.0k wrote:

I've used both Broad's JAVA application and clusterProfiler's R implementation of GSEA and recommend it as performing the same analysis and producing near identical charts. Also, if you adopt it, there are a a bunch of other analyses and visualizations which become available with single setup (e.g. GO & Kegg, in addition to GSEA). I find the documentation a little terse, but everything is there you will need.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Malcolm.Cook1.0k

Thanks, Malcolm ! Just came across EnrichmentBrowser, that seems to have implemented lots of algorithms :

https://bioconductor.org/packages/release/bioc/html/EnrichmentBrowser.html

ADD REPLYlink written 5 months ago by Bogdan720
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