PARADIGM (PAthway Representation and Analysis by DIrect reference on Graphical Models) is a factor graph framework for pathway inference on high-throughput genomic data.

PARADIGM uses environment modules. Type

module load paradigm

then type paradigm at the prompt:

$ paradigm

Examples are available in $PARADIGMHOME/testdata/.

$ cp -R $PARADIGMHOME/testdata .
cd testdata
./runtests.sh

Documentation

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Bioinformatics. 2010 Jun 15;26(12):i237-45. doi: 10.1093/bioinformatics/btq182.

github:Paradigm