PathNet

An R package for pathway analysis using topological information

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("PathNet")

To cite this package in a publication, start R and enter:

    citation("PathNet")

Documentation

PDF R Script PathNet
PDF   Reference Manual

Details

biocViews DifferentialExpression, MultipleComparison, Pathways, Software
Version 1.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL-3
Depends R (>= 1.14.0)
Imports
Suggests PathNetData, RUnit, BiocGenerics
System Requirements
URL
Depends On Me
Imports Me
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Package Downloads

Package Source PathNet_1.5.0.tar.gz
Windows Binary PathNet_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) PathNet_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
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