nCOP is a simple but powerful tool for uncovering cancer-related genes using biological
network information and individual mutational profiles. It balances identifying a small
subset of genes connected in the network with covering a large fraction of the patients.
You can read the full paper here.
You can download nCOP from here.
To run it you need to provide a file specifying the network and a mutational file
containing genes with list of individuals that have variants in these genes.
Sample input files that we used in our study of
Kidney Renal Clear Cell Carcinoma and the HPRD network are included. Please, see the README for
details about any of the additional parameters you can specify. Below is a diagram describing
the nCOP's pipeline.
For questions please contact nCOP's developer Borislav Hristov: borislav(at)cs.princeton.edu.