HyperModules App
Description
Hypermodules is a local graph search algorithm designed by Juri Reimand and Gary Bader. It was implemented in a command line version and as an app for Cytoscape 3.0 as part of Google Summer of Code 2013. Given a gene/protein interaction network, a set of mutation data with associated patients, and a set of clinical patient data, the algorithm aims to find modules within the interaction network most correlated with a clinical outcome. In particular, survival times are analyzed using the log rank test for survival curve comparison, and fisher's exact test is used for discrete clinical variables. Only pSNV's are considered, and the algorithm can be applied to many clinical variables. For more info, please consult the original paper; the algorithm is described in the second half.
Command-Line Version
The lightweight version is implemented
Cytoscape App Version