How to run PARADIGM

Five3 Genomics maintains a webpage with documentation about how to run PARADIGM. Visit THIS PAGE to get started.

For more advanced users, there is a tutorial using wrapper scripts for running PARADIGM jobs. The tutorial is here.

The scripts require the 2010 public version of the binary available here. The citation for this version is:

Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M. Stuart; Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics, Volume 26, Issue 12, 15 June 2010, Pages i237–i245,