NetPathMiner

DOI: 10.18129/B9.bioc.NetPathMiner  

NetPathMiner for Biological Network Construction, Path Mining and Visualization

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	NetPathMiner Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, GraphAndNetwork, Network, Pathways, Software
Version	1.34.2
In Bioconductor since	BioC 2.14 (R-3.1) (9 years)
License	GPL (>= 2)
Depends	R (>= 3.0.2), igraph (>= 1.0)
Imports
LinkingTo
Suggests	rBiopaxParser(>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle
SystemRequirements	libxml2, libSBML (>= 5.5)
Enhances
URL	https://github.com/ahmohamed/NetPathMiner
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	NetPathMiner_1.34.2.tar.gz
Windows Binary	NetPathMiner_1.34.2.zip
macOS Binary (x86_64)	NetPathMiner_1.34.2.tgz
macOS Binary (arm64)
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 3.16	Source Archive