Software

A script that uses patterns of recurrence and mutual exclusivity to identify functional modules in tumors. The tool will build a weighted graph using the Winnow algorithm, then search it for modules that are highly recurrent (across samples) and have high levels of mutual exclusivity. The significance of these patterns is determined using the algorithmic significance test.

Requires bash and ruby See README for more information.

Author: Chris Miller (chrisamiller@gmail.com)
Version: 1.0
License: MIT
Download: rmeMod.tar.gz
Reference:
Miller, Christopher A., Settle, Stephen H., Sulman, Erik P., Aldape, Kenneth D., and Milosavljevic, Aleksandar. Discovering functional modules relevant for cancer progression by identifying patterns of recurrent and mutually exclusive aberrations in tumor samples. (In Submission)