[BioC] GO categories in R for A. Thaliana

Marc Carlson mcarlson at fhcrc.org
Fri Jul 10 17:55:38 CEST 2009

Hi Vishal,

We have an organism level package for Arabidopsis in the development branch:


Please let us know if you find it satisfactory or not (it's new).

Also, if you have general question about GO ontologies, you might want
to look at the basic GO usage vignette here:


And if you want to do some hypergeometric testing you might want to look
at the GOstats package:


Hope this helps,


Vishal Thapar wrote:
> Dear Listers,
> I had a small query. I am working with A. Thaliana and after some initial
> analysis I have a list of genes (2000 or so). I want to now classify them
> into GO categories. I know there are lots of web based tools to do this but
> I want to do this in R. Has anyone done this before ? (I am sure, someone
> has, or so I hope) I tried to look around but I didn't find any whole genome
> annotation package like "org.Hs.eg.db" for Arabidopsis Thaliana. I found
> this on BioC
> http://bioconductor.org/packages/2.2/Arabidopsis_thaliana.html
> But it does not seem like I can use this for my GO term analysis. Does
> anyone know of a package in R that can be used for Arabidopsis? Any pointers
> and help would be greatly appreciated.
> Thanks,
> Sincerely,
> Vishal

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