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("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 | ||
| 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 |