This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization

Bioconductor version: Release (3.17)

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 "4.3") 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 1.36.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 years)
License GPL (>= 2)
Depends R (>= 3.0.2), igraph (>= 1.0)
Imports
Linking To
Suggests rBiopaxParser(>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle
System Requirements libxml2, libSBML (>= 5.5)
Enhances
URL https://github.com/ahmohamed/NetPathMiner
See More
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_1.36.0.tar.gz
Windows Binary NetPathMiner_1.36.0.zip (64-bit only)
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
Bioc Package Browser https://code.bioconductor.org/browse/NetPathMiner/
Package Short Url https://bioconductor.org/packages/NetPathMiner/
Package Downloads Report Download Stats