[BioC] Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?

[Steve Lianoglou]

Hi,

On Wed, Dec 18, 2013 at 6:20 PM, Zhi-Qiang Ye <yezhiqiang at gmail.com> wrote:
> Hi, all
>
>         I need to analysis genes whose chromosomal locations are based on
> the rat genome version rn4, so installed 'org.Rn.eg.db'. However, the
> genome coordinate system is based on rn5.
>
>          Is there any way to get and install old versions of
> 'org.Rn.eg.db'?

You might consider building a TranscriptDb object from rn4 annotations
using the GenomicFeatures package:

http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html

Read through its vignette to figure out how to download and build a
TranscriptDb from UCSC. It's going to be something like:

R> library(GenomicFeatures)
R> txdb <- makeTranscriptDbFromUCSC(genome='rn4', tablename='ensGene')

Keep reading to figure out how to lookup genes/transcripts by
(ensembl) transcript IDs, and I think you should be good to go.

If you need to do sequence related analyses using these annotations,
you can use the rn4 BSgenome object, to boot:

http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Rnorvegicus.UCSC.rn4.html

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech