PathNet

DOI: 10.18129/B9.bioc.PathNet    

An R package for pathway analysis using topological information

Bioconductor version: Release (3.13)

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 hms.harvard.edu>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PathNet")

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

Documentation

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

browseVignettes("PathNet")

 

PDF R Script PathNet
PDF   Reference Manual

Details

biocViews DifferentialExpression, KEGG, MultipleComparison, Network, NetworkEnrichment, Pathways, Software
Version 1.32.0
In Bioconductor since BioC 2.12 (R-3.0) (8.5 years)
License GPL-3
Depends
Imports
LinkingTo
Suggests PathNetData, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PathNet_1.32.0.tar.gz
Windows Binary PathNet_1.32.0.zip
macOS 10.13 (High Sierra) PathNet_1.32.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PathNet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PathNet
Package Short Url https://bioconductor.org/packages/PathNet/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: