[BioC] GOstats-compatible annotation package for Helicobacter pylori 26995

Marc Carlson mcarlson at fhcrc.org
Tue Oct 14 19:39:43 CEST 2008

Hi Klaus-Peter,

The normal way to make annotation packages is to use the SQLForge
functions in the AnnotationDbi package.  But before you can do that we
have to support that organism with some code to maintain an intermediate
database.  I wish I could tell you that we support H. pylori but we
don't yet.  Currently the only microrganisms we support are E. coli,
yeast and  the malaria parasite.   Perhaps you could help me add H.
pylori to the list of supported organisms?  Please email me about this
so  we can work on a solution together.


Klaus-Peter Pleissner wrote:
> Hi BioC,
> in the BioC-mailing list I have read a lot about annotation packages
> for GOstats or topGO. My question is following:
> 1. Is there already a user-defined GOstats-compatible annotation
> package for Helicobacter pylori 26995  to perform gene enrichment
> analysis using , for instance, hyperGtest ?
> 2. Which package should I use ? GOstats or topGO or are there others,
> too ?
> 3. How to create such new annotation package ? AnnBuilder or other
> R-packages ?
> BTW, for human genes we are using WebGestalt
> (http://bioinfo.vanderbilt.edu/webgestalt/)  to perform gene
> enrichment analysis, but WebGestalt doesn't run for bacterial gene lists.
> Thanks for hints or advices!
> Klaus-Peter

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