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KEGGgraph

This is the development version of KEGGgraph; for the stable release version, see KEGGgraph.

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


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF R Script
KEGGgraph: graph approach to KEGG PATHWAY PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GraphAndNetwork, KEGG, Pathways, Software, Visualization
Version 1.63.0
In Bioconductor since BioC 2.4 (R-2.9) (15 years)
License GPL (>= 2)
Depends R (>= 3.5.0)
Imports methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz
System Requirements
URL http://www.nextbiomotif.com
See More
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
Links To Me
Build Report Build Report

Package Archives

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

Source Package KEGGgraph_1.63.0.tar.gz
Windows Binary KEGGgraph_1.63.0.zip
macOS Binary (x86_64) KEGGgraph_1.63.0.tgz
macOS Binary (arm64) KEGGgraph_1.63.0.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