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NetPathMiner

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of NetPathMiner; for the stable release version, see NetPathMiner.

NetPathMiner for Biological Network Construction, Path Mining and Visualization


Bioconductor version: Development (3.19)

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 [aut, cre] , Tim Hancock [aut], Tim Hancock [aut]

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.39.1
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_1.39.1.tar.gz
Windows Binary NetPathMiner_1.39.1.zip
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/NetPathMiner/
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