bioconductor-pathnet

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PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.

Home http://bioconductor.org/packages/3.6/bioc/html/PathNet.html
Versions 1.16.0, 1.18.0
License GPL-3
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-pathnet

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-pathnet

and update with:

conda update bioconductor-pathnet

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-pathnet.