NetPathMiner

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see NetPathMiner.

NetPathMiner for Biological Network Construction, Path Mining and Visualization

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0001-6507-5300 , 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Clustering, GraphAndNetwork, Network, Pathways, Software

Version 1.44.0

In Bioconductor since BioC 2.14 (R-3.1) (11.5 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

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_1.44.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) NetPathMiner_1.44.0.tgz

macOS Binary (arm64) NetPathMiner_1.44.0.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