
Thanks a lot for your suggestion. I will for sure have a look and inform 
you.
Bests,
Nooshin


On 04/24/2012 04:15 PM, Tim Triche, Jr. wrote:
> Ah, I see.  GSL is a useful library to have installed regardless. 
>  Hope things work out.  I found your exchanges with Paul to be useful 
> reading, but obviously I was not reading closely enough, since Paul 
> started off his code sample with biocLite('MotIV').  Oops :-o
>
> Here is a paper that I found interesting, which does go into some 
> detail towards a "bulk" approach, from Gottardo's group:
>
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016432
>
> Perhaps it will be useful to you as well, would be curious to hear if so.
>
> --t
>
> On Tue, Apr 24, 2012 at 7:00 AM, nooshin <n_omranian@yahoo.com 
> <mailto:n_omranian@yahoo.com>> wrote:
>
>
>     Thanks, it's been already solved, it needs GSL package, which is a
>     bit problematic, but I solved it already.
>
>     But it does include only 5 matrices (in the webpage) for
>     arabidopsis and in the package also!
>     I'm downloading manually from AthaMap!
>
>     Thanks again and keep waiting for 'bulk' approach.
>
>     Bests,
>     Nooshin
>
>
>     On 04/24/2012 03:16 PM, Tim Triche, Jr. wrote:
>>     source("http://bioconductor.org/biocLite.R")
>>     biocLite("MotIV")
>>
>>     ought to do the trick for you
>>
>>
>>
>>     On Tue, Apr 24, 2012 at 1:01 AM, nooshin <n_omranian@yahoo.com
>>     <mailto:n_omranian@yahoo.com>> wrote:
>>
>>
>>         Hi Paul,
>>
>>         Thanks a lot.
>>         I forgot to include bioc, since I only replied to you (no to
>>         all).
>>
>>         I can"t install MotIV package to check. I checked in google but I
>>         couldn't find any solution! Do you have any suggestion for
>>         installing
>>         this package?
>>
>>         Bests,
>>         Nooshin
>>
>>         On 04/23/2012 06:35 PM, Paul Shannon wrote:
>>         > (redirecting this back to the Bioc list…)
>>         >
>>         > Hi Nooshin,
>>         >
>>         > The 'bulk' approach is not quite so ready as I predicted.
>>          I might have something by the end of the week.
>>         >
>>         > As for mapping between PWMs and TFs, I have most often done
>>         this with 'tom-tom' from the meme website.
>>         >
>>         > But I just discovered what looks like a good -- maybe
>>         better -- approach:  the Bioconductor MotIV package, which
>>         includes a 2010 version of jasper.
>>         > Try this:
>>         >
>>         >     source("http://bioconductor.org/biocLite.R")
>>         >
>>         > biocLite ('MotIV')
>>         > library (MotIV);
>>         > browseVignettes ('MotIV')
>>         >
>>         > The jaspar data in this package has 130 TF-PWM mappings,
>>         which appear to be human.  More must be known, and publicly
>>         available.  The JASPAR website has a 'JASPAR CORE Plantae'
>>          data set that
>>         >     - is probably what you are interested in
>>         >     - might be downloadable, and convertible to the form
>>         MotIV wants.
>>         >
>>         > Perhaps other readers of the list have other suggestions.
>>         >
>>         > If you have any questions on this, please include 'BioC' in
>>         your reply, so that we can all get better at this!
>>         >
>>         >   - Paul
>>         >
>>         >
>>         > On Apr 23, 2012, at 6:53 AM, nooshin wrote:
>>         >
>>         >> Hi Paul,
>>         >>
>>         >> Many thanks for your comprehensive information and code!
>>         >> I have a question regarding to extract of PWMs. How and
>>         where I can download these matrices for all TFs that PWM is
>>         available for them? I need it only for Arabidopsis thaliana.
>>         >> Is there any package in R which I can give the TF and
>>         receive the PWM for it? Or any online database which I can
>>         download from it? I have a big problem since Friday to find
>>         out these matrices for different TFs of A.th. That would be
>>         so great if you can help me to get these matrices.
>>         >>
>>         >>> If you want to do this in bulk, Herve' has some lovely
>>         code to make that efficient.
>>         >> Also can I have this? :)
>>         >>
>>         >>
>>         >> Thanks a lot in advance.
>>         >> Best regards,
>>         >> Nooshin
>>         >>
>>         >>
>>
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>>
>>     -- 
>>     /A model is a lie that helps you see the truth./
>>     /
>>     /
>>     Howard Skipper
>>     <http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>>
>
>
>
>
> -- 
> /A model is a lie that helps you see the truth./
> /
> /
> Howard Skipper 
> <http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>


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