Resources

Docker Hub
Stuart Lab on Docker Hub
pCHIPS
Patient Cancer Hallmark Integrated Phospho Signature
PARADIGM
Pathway Recognition Algorithm using Data Integration on Genomic Models
PARADIGM scripts
Wrapper scripts for running paradigm jobs.
PathMark scripts
Scripts for running PathMark.
Paradigm-Shift scripts
Scripts for running Paradigm-Shift.

SCIMITAR
  Tracing co-regulatory network evolution in noisy, single-cell transcriptome trajectories

 

TieDIE
Identify linking networks and pathways between sets of functionally related genes with the Tied Diffusion of Interacting Events (TieDIE) algorithm.
The Interaction Browser
The Interaction Browser is a web-application for visualizing biological pathways and networks.
Cluegene
Cluegene is a collaborative filtering-based gene recommendation system which uses pre-computed clusters of genes to recommend new genes for a query pathway.