PathNet

DOI: 10.18129/B9.bioc.PathNet  

An R package for pathway analysis using topological information

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	1.38.0
In Bioconductor since	BioC 2.12 (R-3.0) (10 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_1.38.0.tar.gz
Windows Binary	PathNet_1.38.0.zip
macOS Binary (x86_64)	PathNet_1.38.0.tgz
macOS Binary (arm64)	PathNet_1.38.0.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/
Package Downloads Report	Download Stats