[BioC] Running the GSEA algorithm

[Steve Lianoglou]

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