To install this package, start R and enter:

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

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

NetPathMiner

 

NetPathMiner for Biological Network Construction, Path Mining and Visualization

Bioconductor version: Release (3.1)

NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.

Author: Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>, Tim Hancock <timothy.hancock at kuicr.kyoto-u.ac.jp>, Ichigaku Takigawa <takigawa at kuicr.kyoto-u.ac.jp>, Nicolas Wicker <nicolas.wicker at unistra.fr>

Maintainer: Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>

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

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NetPathMiner")

 

PDF R Script NetPathMiner Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Clustering, GraphAndNetwork, Network, Pathways, Software
Version 1.4.1
In Bioconductor since BioC 2.14 (R-3.1) (1.5 years)
License GPL (>= 2)
Depends R (>= 3.0.2), igraph (>= 1.0)
Imports
LinkingTo
Suggests rBiopaxParser(>= 2.1), RCurl, RCytoscape, graph
SystemRequirements libxml2, libSBML (>= 5.5)
Enhances
URL https://github.com/ahmohamed/NetPathMiner
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source NetPathMiner_1.4.1.tar.gz
Windows Binary NetPathMiner_1.4.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) NetPathMiner_1.4.1.tgz
Mac OS X 10.9 (Mavericks) NetPathMiner_1.4.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/NetPathMiner/tree/release-3.1
Package Short Url http://bioconductor.org/packages/NetPathMiner/
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