[BioC] Running the GSEA algorithm

[Ryan]

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
>>>
>>
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>
>