[BioC] GSEA for R

[Sylvain Brohée]

Le 25/06/2013 18:52, Sylvain Brohée a écrit :
> Le 25/06/2013 18:52, Sylvain Brohée a écrit :
>> Hi January,
>>
>> I recently discovered the nice package "piano" for bioconductor. It 
>> is very easy to use and displays the results in a very nice way.
>>
>> http://bioconductor.org/packages/release/bioc/html/piano.html
>>
>> I also developped my own GSEA tool (web). It works in C++ (multicore) 
>> and R. That can maybe interest you. If you wish, I can provide you 
>> with the code.
>>
>> http://rsat.bigre.ulb.ac.be/~sylvain/new_gsea/php/
>>
>> Cheers,
>>
>> Sylvain
>>
>>
>> Le 25/06/2013 16:18, January Weiner a écrit :
>>> GSEA is an algorithm for testing gene set enrichment. It is
>>> distributed as a Java standalone program or an R script; however the R
>>> script is (a) crippled and (b) not straightforward to use (not really
>>> written "the R way").
>>>
>>> However, the algorithm itself seems interesting, since it (a) does not
>>> require arbitrary thresholds for selecting the enriched gene set and
>>> (b) uses a permutation approach to assess the significant changes for
>>> GOs, and so directly takes into account the actual variability of the
>>> data.
>>>
>>> What alternative presents itself for R?
>>>
>>> kind regards,
>>>
>>> January
>>>
>>
>