KEGGgraph
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see KEGGgraph.
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
Bioconductor version: 3.11
KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
Author: Jitao David Zhang, with inputs from Paul Shannon
Maintainer: Jitao David Zhang <jitao_david.zhang at roche.com>
citation("KEGGgraph")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("KEGGgraph")
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("KEGGgraph")| KEGGgraph: Application Examples | R Script | |
| KEGGgraph: graph approach to KEGG PATHWAY | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, KEGG, Pathways, Software, Visualization |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (15 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0) |
| Imports | methods, XML (>= 2.3-0), graph, utils, RCurl |
| System Requirements | |
| URL | http://www.nextbiomotif.com |
See More
| Suggests | Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA |
| Linking To | |
| Enhances | |
| Depends On Me | ROntoTools, SPIA |
| Imports Me | clipper, DEGraph, EnrichmentBrowser, KEGGlincs, MAGeCKFlute, MetaboSignal, MWASTools, NCIgraph, pathview |
| Suggests Me | DEGraph, GenomicRanges |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | KEGGgraph_1.48.0.tar.gz |
| Windows Binary | KEGGgraph_1.48.0.zip |
| macOS 10.13 (High Sierra) | KEGGgraph_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/KEGGgraph |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/KEGGgraph |
| Bioc Package Browser | https://code.bioconductor.org/browse/KEGGgraph/ |
| Package Short Url | https://bioconductor.org/packages/KEGGgraph/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |