To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("PathNet")

In most cases, you don't need to download the package archive at all.

PathNet

 

An R package for pathway analysis using topological information

Bioconductor version: Release (3.1)

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: Jason B. Smith <jsmith at bhsai.org>

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

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("PathNet")

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 1.8.0
In Bioconductor since BioC 2.12 (R-3.0) (2.5 years)
License GPL-3
Depends R (>= 1.14.0)
Imports
LinkingTo
Suggests PathNetData, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me EnrichmentBrowser
Suggests Me
Build Report  

Package Archives

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

Package Source PathNet_1.8.0.tar.gz
Windows Binary PathNet_1.8.0.zip
Mac OS X 10.6 (Snow Leopard) PathNet_1.8.0.tgz
Mac OS X 10.9 (Mavericks) PathNet_1.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/PathNet/tree/release-3.1
Package Short Url http://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:

Fred Hutchinson Cancer Research Center