Hi Giuseppe,

You're probably looking for something like Cummerbund:

http://compbio.mit.edu/cummeRbund/

which has a wrapper in the tool shed:

http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund

This isn't on our public server yet, but it may be added in the future. You 
might look into using Galaxy Cloud, where you can add tools to your instance:

http://wiki.galaxyproject.org/CloudMan

Good luck,
J.


On Mar 22, 2013, at 7:04 PM, Ianiri, Giuseppe wrote:

> Hello,
> I performed my mapping using tophat - cufflink - cuffmerge - cuffdiff.
> With the information I have for my analysis so far, I can reannotate wrong
> genes, check for correct splicing etc. However, I would like to perform
> some analysis post-alignment, like for example samples clustering, volcano
> plot, heat maps etc. I guess I can't do this kind of analysis with Galaxy
> (I am using the free version on line on my Windows laptop) since I haven't
> found anything in the tools section. Does anyone know a software that I
> could use in windows with the data obtained in Galaxy?
> Any suggestion is really appreciated.
> Regards,
> 
> Giuseppe
> 
> 
> 
> 
> Giuseppe Ianiri, Ph.D.
> Division of Cell Biology and Biophysics
> School of Biological Sciences
> 5100 Rockhill Road
> University of Missouri-Kansas City
> Kansas City, MO 64110
> Email: iani...@umkc.edu
> 
> 
> 
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___________________________________________________________
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