[BioC] any good R package to scan microRNA target?

Steve Lianoglou mailinglist.honeypot at gmail.com
Fri Mar 16 20:23:42 CET 2012


On Fri, Mar 16, 2012 at 3:18 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> On Fri, Mar 16, 2012 at 3:15 PM, wang peter <wng.peter at gmail.com> wrote:
>> no,
>> it is not so simple
>> there are many algorithms to scan microRNA on 3'UTR
>> NOT match,
>> SOME people call it miRNA target prediction
>> like picTar or miRanda
> It's true -- and SOME people don't really put too much faith in such
> predictions, is what I'm saying (that's where my "some (¿any?) of
> story" comment came from ;-)
> But anyway -- so you're looking for an R wrapper to picTar, or
> miRanda, or targetscan, or mirSVR, or?

I bet you'd get pretty close to such methods by doing a seed match (w/
or w/o m1A rule) and filter by conservation if you want to do some
type of analysis (functional enrichments of "targets", or something).

If you want to do better, see if you can't encourage your
collaborators to do some type of differential *-CLIP experiment ...
more data == more fun :-)


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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