[BioC] BioC package for miRNA target scanning (or displaying results from databases)

[James F.Reid]

Hi Kart,

Karthik K N <karthikuttan at ...> writes:

> 
> Dear Members,
> 
> Are there packages for searching miRNA targets in Bioconductor?
> 
> I Have a list of miRNAs each of whose common target I want to pull out from
> TargetScan, PicTar, miRanda, miRDB etc.  Is this really possible?
> 
> As a last resort, which BioC/R package can help me search the
> aforementioned databases and save the targets (that is common to all the
> databases) in a txt or excel format?

you could try the BioC RmiR and RmiR.Hs.miRNA packages which integrate different
databases of predicted human gene targets alternatively use an on-line tool such
as mirDIP <http://ophid.utoronto.ca/mirDIP/search.jsp> for example.
The only single database that is available on BioC is targetscan for human and
mouse only ('targetscan.Hs.eg.db', 'targetscan.Mm.eg.db').
HTH.
J.

> 
> It is taking hell lot of time searching all databases!
> 
> Thanks a lot,
> 
> Regards,
> 
> Kart
>