What is Genecentric?
Genecentric is a package that performs two main tasks:
- Implement the between-pathway module (BPM) generation algorithm with pruning as described in Leiserson et al, 2010. In particular, the implementation is automatically parallelized when more than one CPU is present.
- Perform GO enrichment on generated BPMs using the JSON-RPC API of FuncAssociate 2.0.
Genecentric is completely configurable via the command line.
How do I use it?
Here's a quick example of generating BPM's using the Collins et al dataset from the Krogan Lab Interactome Database.
genecentric-bpms yeast_emap.gi output.bpm
And to perform GO enrichment on 'output.bpm', simply use:
genecentric-go yeast_emap.gi output.bpm enrichment.gobpm
Windows users will need to prefix each of the above commands with their python2 interpreter. Like this:
C:\Python2.7\python.exe genecentric-bpms ...
Dependencies?
If you have Python 2.7, that should be enough to get Genecentric up and and running. No other dependencies are required.
If you're running Python 2.6, you'll need to install the 'argparse' module from PyPI. If you have 'easy_install' installed, it should be as simple as:
easy_install-2.6 argparse
And Genecentric should work after that.
We don't currently support Python versions older than 2.6.