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An R package for pathway analysis using topological information

Bioconductor version: Release (3.18)

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.

Author: Bhaskar Dutta <bhaskar.dutta at gmail.com>, Anders Wallqvist <awallqvist at bhsai.org>, and Jaques Reifman <jreifman at bhsai.org>

Maintainer: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>

Citation (from within R, enter citation("PathNet")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

PathNet PDF R Script
Reference Manual PDF


biocViews DifferentialExpression, KEGG, MultipleComparison, Network, NetworkEnrichment, Pathways, Software
Version 1.42.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License GPL-3
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Suggests PathNetData, RUnit, BiocGenerics
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Follow Installation instructions to use this package in your R session.

Source Package PathNet_1.42.0.tar.gz
Windows Binary PathNet_1.42.0.zip
macOS Binary (x86_64) PathNet_1.42.0.tgz
macOS Binary (arm64) PathNet_1.42.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PathNet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PathNet
Bioc Package Browser https://code.bioconductor.org/browse/PathNet/
Package Short Url https://bioconductor.org/packages/PathNet/
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