[BioC] Running the GSEA algorithm

Julian Gehring julian.gehring at embl.de
Tue Apr 1 09:50:17 CEST 2014


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 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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