This is the Python implementation of the cMonkey algorithm based on the original R implementation by David Reiss, Institute for Systems Biology

Testing

• Developed and tested with Python 2.7.2
• scipy >= 0.9.0
• numpy >= 1.6.0
• MySQLdb >= 1.2.3
• BeautifulSoup >= 3.2.0
• R >= 2.14.1
• rpy2 >= 2.2.1
• MEME 4.3.0
• csh (for running MEME) for the human setup, Weeder 1.4.2 is needed

./run_tests.sh

In general, you should be able to run cmonkey-python on microbial gene expressions with

./run_cmonkey.sh <organism-code> <tab separated file of gene expressions>

The file can be either in your file system or a web URL.

There is a startup script for cMonkey to run the current integrated system

./run_cmonkey.sh hal halo_ratios5.tsv