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

[Marc Carlson]

Steve is right.  You could go and do that.  However in this case we have 
already done the work for you.  You can find a package here:

http://www.bioconductor.org/packages/release/data/annotation/html/TxDb.Rnorvegicus.UCSC.rn4.ensGene.html

That should get you transcript locations for RN4.

For more information about how you can make use of that resource and of 
others like it, please be sure to also peak at our workflow:

http://www.bioconductor.org/help/workflows/annotation/annotation/


   Marc




On 12/18/2013 10:09 PM, Steve Lianoglou wrote:
> 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
>