Software

An R package for Multi-Omics data integration and visualization

Parallel Mutual Information Estimation for Gene Network Reconstruction

An R package for the identification of significant signal paths within significantly altered biological pathways.

graphite (GRAPH Interaction from pathway Topological Environment) is a computational framework to store, parse and convert pathway topologies to gene-gene networks.

An R pipeline to perform topological pathway analysis integrating gene and miRNA expression profiles

R package for multi-omic topological pathway analysis looking for survival-associated gene modules

A scalable normalization for single-cell RNA-seq data

a new method for simulating data from perturbed biological PATHways

A Graphical Model Approach to Identify Primary Genes in Perturbed Biological Pathways

Gene Set Analysis Exploiting Pathway Topology