To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("KEGGgraph")

In most cases, you don't need to download the package archive at all.

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 (3.3)

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("KEGGgraph")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("KEGGgraph")

 

PDF KEGGgraph: Application Examples
PDF KEGGgraph: graph approach to KEGG PATHWAY
PDF   Reference Manual
Text   NEWS

Details

biocViews GraphAndNetwork, KEGG, Pathways, Software, Visualization
Version 1.29.0
In Bioconductor since BioC 2.4 (R-2.9) (7 years)
License GPL (>= 2)
Depends
Imports methods, XML (>= 2.3-0), graph
LinkingTo
Suggests Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA
SystemRequirements
Enhances
URL http://www.nextbiomotif.com
Depends On Me ROntoTools, SPIA
Imports Me clipper, DEGraph, EnrichmentBrowser, NCIgraph, pathview, ToPASeq
Suggests Me DEGraph, GenomicRanges
Build Report  

Package Archives

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

Package Source KEGGgraph_1.29.0.tar.gz
Windows Binary KEGGgraph_1.29.0.zip
Mac OS X 10.6 (Snow Leopard) KEGGgraph_1.27.2.tgz
Mac OS X 10.9 (Mavericks) KEGGgraph_1.29.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/KEGGgraph
Package Short Url http://bioconductor.org/packages/KEGGgraph/
Package Downloads Report Download Stats

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