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Gene set enrichment analysis

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

gsa gsea enrichment r
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updated by zx8754 zx8754 • written by Bogdan Bogdan

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

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written by Ram Ram

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/")
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updated by Ram Ram • written by Bogdan Bogdan

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.

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written by Ram Ram

Thanks a lot, Ram !

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

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written by Bogdan Bogdan

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.)

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written by Trypto • Trypto

1 answer

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.

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written by Malcolm.Cook Malcolm.Cook

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