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 (2.14)

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 1.0.4
In Bioconductor since BioC 2.14 (R-3.1)
License GPL (>= 2)
Depends R (>= 3.0.2), igraph (>= 0.6)
Imports
Suggests rBiopaxParser(>= 2.1), RCurl, RCytoscape
System Requirements libxml2, libSBML (>= 5.5)
URL https://github.com/ahmohamed/NetPathMiner
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source NetPathMiner_1.0.4.tar.gz
Windows Binary NetPathMiner_1.0.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) NetPathMiner_1.0.4.tgz
Mac OS X 10.9 (Mavericks) NetPathMiner_1.0.4.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center