[BioC] Small RNAs database

[Robert Gentleman]

Sean Davis wrote:
> On Fri, Jul 11, 2008 at 6:01 AM, Daniel Brewer <daniel.brewer at icr.ac.uk> wrote:
>> Hi,
>>
>> Not strictly bioconductor related, so apologies, but I was wondering
>> whether anyone knew of a good all encompassing small RNAs database.  I
>> would like to find all small RNAs (RNAis etc.) within a particular
>> genomic region.
> 
> I would take a look at the UCSC genome browser track for small RNAs,
> which includes snoRNAs as well as miRNAs (and a few others).  I do not
> know of another resource that combines all the data this way.  It is
> quite easy to make a custom track that includes your regions of
> interest and to then extract using the table browser the information
> that overlaps your custom track.  Alternatively, you can download the
> entire track (I think it is the wgRNA table, if I remember correctly)
> and process in R.

   And of course there is the new-ish rtracklayer package that can help 
you to do most of that..

   best wishes
     Robert

> 
> Sean
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org