NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

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

Documentation

PDF R Script NetPathMiner Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Clustering, GraphAndNetwork, Network, Pathways, Software
Version 1.1.6
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 Downloads

Package Source NetPathMiner_1.1.6.tar.gz
Windows Binary NetPathMiner_1.1.6.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) NetPathMiner_1.1.6.tgz
Mac OS X 10.9 (Mavericks) NetPathMiner_1.1.6.tgz
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