Isn't the existing GeneSetEnrichment biocView sufficient? It's nested under Software>Bioinformatics>Enrichment in release and Software>BiologicalQuestion> in devel. All the best Leif On Mon, Mar 31, 2014 at 11:01 PM, Ryan wrote: > Yes, I think that would be helpful. There are a *lot* of these packages, > and it would be useful to have a comprehensive list. > > > On Mon Mar 31 14:00:01 2014, Steve Lianoglou wrote: > >> Hi, >> >> It's great to see all of these other packages popping out of the wood >> work. >> >> Bioc folks: Makes me wonder if we should add a GSEA biocView to help >> identify these more quickly ... I think it'd be handy. >> >> -steve >> >> >> On Mon, Mar 31, 2014 at 1:00 PM, Julian Gehring >> wrote: >> >>> Hi Enrico, >>> >>> You can also have a look at the GSRI package: >>> http://bioconductor.org/packages/release/bioc/html/GSRI.html >>> >>> Best wishes >>> Julian >>> >>> >>> On 31/03/14 21:19, Enrico Ferrero wrote: >>> >>>> Hi everyone, >>>> >>>> I would like to include GSEA into my R analytical pipelines, but I'm >>>> struggling to understand what's the best way to implement it. The >>>> following >>>> information might be incomplete or even wrong, but here is what I >>>> understood so far: >>>> >>>> - The GSEABase package [1] provides an excellent infrastructure for >>>> dealing >>>> with gene sets and gene sets collections but, as far as I understand, >>>> doesn't provide a way to run the GSEA algorithm. >>>> >>>> - The PGSEA package [2] provides a minimal, and perhaps simplistic, >>>> interface to GSEA. It does run the analysis but only outputs a matrix >>>> with >>>> what I understand is a score (possibly the NES?) and nothing else. >>>> >>>> - The SeqGSEA package [3] allows to run the GSEA algorithm and also >>>> produces some excellent plots of gene sets enrichment. However, it works >>>> with with RNA-seq count data and I don't see how it could be adapted to >>>> microarray data. >>>> >>>> - The GSEA-P-R package from the Broad Institute [4] is arguably not >>>> ideal >>>> to work with and its use is basically discouraged. >>>> >>>> - The Java version of GSEA [4] is probably my best bet at the moment, >>>> as it >>>> allows command-line usage and provides a complete output for the >>>> analysis. >>>> >>>> So, am I missing something here? >>>> Is there an established way to run the GSEA algorithm from R using >>>> Bioconductor packages that also works for non-NGS data? >>>> If not, would anybody recommend the GSEA-P-R package from the Broad >>>> Institute? >>>> Are there any other options? >>>> >>>> Thanks very much. >>>> Best, >>>> >>>> [1] http://www.bioconductor.org/packages/release/bioc/html/ >>>> GSEABase.html >>>> [2] http://www.bioconductor.org/packages/release/bioc/html/PGSEA.html >>>> [3] http://www.bioconductor.org/packages/release/bioc/html/SeqGSEA.html >>>> [4] http://www.broadinstitute.org/gsea/downloads.jsp >>>> >>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane. >>> science.biology.informatics.conductor >>> >> >> >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > [[alternative HTML version deleted]]