Many thanks for the information.


On Fri, Jan 31, 2014 at 10:22 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> On Fri, Jan 31, 2014 at 12:14 PM, Orcun Hacariz <orcunhacariz@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
>

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