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 code repository the contains wrapper scripts for running PARADIGM jobs. The code repository is at GitHub.
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, https://doi.org/10.1093/bioinformatics/btq182