KEGGgraph

This is the released version of KEGGgraph; for the devel version, see KEGGgraph.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

Bioconductor version: Release (3.23)

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 and Hervé Pagès

Maintainer: Jitao David Zhang <jitao_david.zhang at roche.com>

Citation (from within R, enter citation("KEGGgraph")):

Jitao David Zhang, with inputs from Paul Shannon and Hervé Pagès. KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor. doi:10.18129/B9.bioc.KEGGgraph, R package version 1.72.0, https://bioconductor.org/packages/KEGGgraph.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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: graph approach to KEGG PATHWAY	PDF	R Script
KEGGgraph: Application Examples	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GraphAndNetwork, KEGG, Pathways, Software, Visualization
Version	1.72.0
In Bioconductor since	BioC 2.4 (R-2.9) (17.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0)
Imports	methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz
System Requirements
URL	https://accio.github.io/research/#software

Suggests	RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA
Linking To
Enhances
Depends On Me	lpNet, ROntoTools, SPIA
Imports Me	clipper, DEGraph, EnrichmentBrowser, KEGGlincs, MetaboSignal, MWASTools, NCIgraph, pathview
Suggests Me	DEGraph, GenomicRanges, kangar00, maGUI, rags2ridges, specmine
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	KEGGgraph_1.72.0.tar.gz
Windows Binary (x86_64)	KEGGgraph_1.72.0.zip
macOS Binary (big-sur-x86_64)	KEGGgraph_1.72.0.tgz
macOS Binary (sonoma-arm64)	KEGGgraph_1.72.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/KEGGgraph
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/KEGGgraph
Package Short Url	https://bioconductor.org/packages/KEGGgraph/
Package Downloads Report	Download Stats