[BioC] BioC 2.5 and BSgenome.Hsapiens.UCSC.hg19

[Hervé Pagès]

Hi Steve,

Steve Lianoglou wrote:
> Hi all,
> 
> I'm using R 2.10-devel w/ BioC 2.5 because I want to get a bit more 
> acquainted w/ the nextgenseq packages. I noticed, however, that the 
> BSgenome.Hsapiens.UCSC.hg19 package isn't in the BioC 2.5 Annotation 
> downloads:
> 
> http://www.bioconductor.org/packages/2.5/data/annotation/
> 
> Is there a particular reason for that besides not having gotten around 
> to it?

No particular reason.

> 
> Can I simply d/l the *.hg19 source package from BioC 2.4 and compile it 
> myself for R 2.10?

Yes, that should work. Some upcoming changes in the underlying containers
that are used to store the chromosome sequences might break backward
compatibility for those BSgenome data packages between BioC 2.4 and 2.5
but for now they are compatible.

H.

> 
> -steve
> 
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>   |  Memorial Sloan-Kettering Cancer Center
>   |  Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
> 
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-- 
Hervé Pagès

Program in Computational Biology
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