PathNet

DOI: 10.18129/B9.bioc.PathNet    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of PathNet; to use it, please install the devel version of Bioconductor.

An R package for pathway analysis using topological information

Bioconductor version: Development (3.10)

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 (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("PathNet")

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

Documentation

PDF   Reference Manual

Details

biocViews DifferentialExpression, KEGG, MultipleComparison, Network, NetworkEnrichment, Pathways, Software
Version 1.25.1
In Bioconductor since BioC 2.12 (R-3.0) (6.5 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
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
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 http://bioconductor.org/packages/PathNet/
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