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 <organism-code> --ratios <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 --organism hal --ratios halo_ratios5.tsv