Running the GSEA algorithm

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Leif Väremo ▴ 70

@leif-varemo-5898

Last seen 9.0 years ago

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 <rct@thompsonclan.org> 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 <julian.gehring@embl.de> >> 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]]

Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI • 2.0k views

ADD COMMENT • link updated 10.7 years ago by Steve Lianoglou ★ 13k • written 10.7 years ago by Leif Väremo ▴ 70

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 22 months ago

United States

aha -- yes, I reckon it would be. Needs some more curation, though, as several of the packages aren't listed there such as: * GSRI * piano * limma (for camera, roast, romer) * PGSEA * ... ? I guess this is the responsibility of the maintainers though, no? -steve On 31 Mar 2014, at 23:57, Leif V?remo wrote: > 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 <rct at="" thompsonclan.org=""> 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 >>> <julian.gehring at="" embl.de=""> >>> 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 at 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 at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >>

ADD COMMENT • link 10.7 years ago Steve Lianoglou ★ 13k

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Hi Steve, Well, some are indeed missing. I just added GSRI to those categories. Best wishes Julian On 01/04/14 09:03, Steve Lianoglou wrote: > aha -- yes, I reckon it would be. > > Needs some more curation, though, as several of the packages aren't > listed there such as: > > * GSRI > * piano > * limma (for camera, roast, romer) > * PGSEA > * ... ? > > I guess this is the responsibility of the maintainers though, no? > > -steve > > On 31 Mar 2014, at 23:57, Leif V?remo wrote: > >> 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 <rct at="" thompsonclan.org=""> 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 >>>> <julian.gehring at="" embl.de=""> >>>> 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 at 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 at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane. >>> science.biology.informatics.conductor >>>

ADD REPLY • link 10.7 years ago Julian Gehring ★ 1.3k

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Thanks everyone for the suggestions, I'm going to test those packages soon. All the best, On 1 April 2014 08:50, Julian Gehring <julian.gehring@embl.de> wrote: > Hi Steve, > > Well, some are indeed missing. I just added GSRI to those categories. > > Best wishes > Julian > > > On 01/04/14 09:03, Steve Lianoglou wrote: > > aha -- yes, I reckon it would be. > > > > Needs some more curation, though, as several of the packages aren't > > listed there such as: > > > > * GSRI > > * piano > > * limma (for camera, roast, romer) > > * PGSEA > > * ... ? > > > > I guess this is the responsibility of the maintainers though, no? > > > > -steve > > > > On 31 Mar 2014, at 23:57, Leif Väremo wrote: > > > >> 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 <rct@thompsonclan.org> 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 > >>>> <julian.gehring@embl.de> > >>>> 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 > >>> > > _______________________________________________ > 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 > -- Enrico Ferrero Department of Genetics Cambridge Systems Biology Centre University of Cambridge [[alternative HTML version deleted]]

ADD REPLY • link 10.7 years ago enricoferrero ▴ 660

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