NetPathMiner

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see NetPathMiner.

NetPathMiner for Biological Network Construction, Path Mining and Visualization


Bioconductor version: 3.9

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 (version "3.6") and enter:


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

BiocManager::install("NetPathMiner")

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

Documentation

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

browseVignettes("NetPathMiner")
NetPathMiner Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, GraphAndNetwork, Network, Pathways, Software
Version 1.20.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL (>= 2)
Depends R (>= 3.0.2), igraph (>= 1.0)
Imports
System Requirements libxml2, libSBML (>= 5.5)
URL https://github.com/ahmohamed/NetPathMiner
See More
Suggests rBiopaxParser(>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package NetPathMiner_1.20.0.tar.gz
Windows Binary NetPathMiner_1.20.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) NetPathMiner_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NetPathMiner
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NetPathMiner
Bioc Package Browser https://code.bioconductor.org/browse/NetPathMiner/
Package Short Url https://bioconductor.org/packages/NetPathMiner/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive