[BioC] Ontology

[Steve Lianoglou]

Hi,

On Fri, Jan 31, 2014 at 12:14 PM, Orcun Hacariz <orcunhacariz at gmail.com> wrote:
> Hi,
>
> My question is how to do a GO analysis with 'genes' using bioconductor
> tools.

OK, in this case there are several packages that you can use to do
different types of GO analyses. You can browse the package available
in bioconductor here:

http://bioconductor.org/packages/release/BiocViews.html#___Software

To make it easier to do so, the bioc-folks have enabled packages to be
tagged by functionality.

There is a drill-down menu on the left hand side of the page you can
use to navigate these tags (aka "Views"). Dig down to:

    Software > Annotation > GO

To filter packages that were annotated to work w/ gene ontologies.

You might try to start with either GOstats or goProflies.

Each package has one (or more) vignettes detailing how they are used
in an analysis, which should get you started.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech