[BioC] GO enrichment on an ordered list of genes

[Steve Lianoglou]

Hi January,

On Mon, Apr 22, 2013 at 3:59 AM, January Weiner
<january.weiner at gmail.com> wrote:
> Hello,
>
> I am aware of two tools that allow to test gene enrichment on an ordered
> list of genes (rather than comparing a set of differentially regulated
> genes with a background list): GOrilla (
> http://cbl-gorilla.cs.technion.ac.il/) and GOstat (
> http://gostat.wehi.edu.au/). Both seem to work pretty well for my purposes,
> but both are only implemented as services available through a web interface.
>
> Is there already any package like this available for R / Bioconductor?

Would GSEA (and similar tests) do the trick for you?

You'll find a few packages in bioc-land to run GSEA-like tests for you
by searching for GSEA in the bioc software page. Hidden in limma is
`romer` which also does similar testing using linear models.
Coincidentally, the author of the new `piano` package posted an
announcement of it being publicly available for use on the bioc-devel
list soon after you posted your question, which you might have missed
-- I haven't used it, but the announcement suggests that it does GSEA
as well, so perhaps another option.

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech