To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PathNet")

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

PathNet

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see PathNet.

An R package for pathway analysis using topological information

Bioconductor version: 2.12

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:// URLs are not supported
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, MultipleComparisons, Pathways, Software
Version	1.0.0
In Bioconductor since	BioC 2.12 (R-3.0) (3 years)
License	GPL-3
Depends	R (>= 1.14.0)
Imports
LinkingTo
Suggests	PathNetData, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source	PathNet_1.0.0.tar.gz
Windows Binary	PathNet_1.0.0.zip
Mac OS X 10.6 (Snow Leopard)	PathNet_1.0.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/PathNet/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/PathNet/
Package Downloads Report	Download Stats

Documentation »

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