[BioC] offline gene name conversion

James W. MacDonald jmacdon at med.umich.edu
Mon Jan 4 19:46:32 CET 2010

Hi Ranier,

Rainer Tischler wrote:
> Dear all,
> I have been using the bioMart and DAVIDQuery R-packages to convert
> gene identifiers into different formats. Unfortunately, both of these
> packages require direct internet access for every conversion. Is
> anybody aware of an R-package or script which supports "offline" gene
> name conversion, i.e. based on previously downloaded gene name
> database files (disk space is no problem)?

It's not clear what you mean by 'gene name conversion', nor do you 
mention the species you are working with, so this is just a stab in the 
dark. But the org.Xx.eg.db packages might be what you are after. For 
instance, if you are working with human samples, the org.Hs.eg.db 
package maps Entrez Gene IDs to various other things including both gene 
names and symbols.



> Many thanks, Rainer
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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