Coexpression Analysis Of Genes Using Python

Question

[pixie@bioinfo]

I know that coexpression analysis can be done in R but I want to know if its possible in Python using expression values of genes. Thanks!

Answer 1

[Devon Ryan]

Sure, just use rpy or rpy2 to use R from python. Alternatively have a look at the WGCNA pipeline, which appears to be a wrapper for WGCNA in python (I presume it uses rpy, but perhaps not).

[Ashutosh Pandey]

It uses rpy2 and you may have to get all the dependencies before you can use the pipeline- rpy2 (http://rpy.sourceforge.net/rpy2), sqlite3, tables (http://www.pytables.org/), Numpy and Cython. I would advise you use WGCNA in R. Its easy to install and their tutorial is pretty simple to use. Also, it really depends on what exactly you want to do? WGCNA is pretty sophisticated but if you just want to some simple clustering I am sure there are many modules in Python for that.