View source code at bitbucket.

MERLIN
An expression-based network inference algorithm that can predict regulators for individual genes and modules.

RIPPLE
A machine learning algorithm for predicting enhancer-promoter interactions

Arboretum
Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.

NIPD
A multiple network learning approach to capture system-wide condition-specific responses.

RENCO
A synthetic regulatory network generator.