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
>>>>
>>>>
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>>
>>
>>
>>
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