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This is the development version of PathNet; for the stable release version, see PathNet.

An R package for pathway analysis using topological information

Bioconductor version: Development (3.20)

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>, Anders Wallqvist <awallqvist at>, and Jaques Reifman <jreifman at>

Maintainer: Ludwig Geistlinger <ludwig.geistlinger at>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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 1.45.0
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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Source Package PathNet_1.45.0.tar.gz
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macOS Binary (x86_64) PathNet_1.45.0.tgz
macOS Binary (arm64) PathNet_1.45.0.tgz
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