KEGGgraph

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("KEGGgraph")

To cite this package in a publication, start R and enter:

    citation("KEGGgraph")

Documentation

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

Details

biocViews GraphAndNetwork, Pathways, Software, Visualization
Version 1.23.1
In Bioconductor since BioC 2.4 (R-2.9)
License GPL (>= 2)
Depends R (>= 2.10), methods, XML (>= 2.3-0), graph
Imports methods, XML, graph
Suggests Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA
System Requirements
URL http://www.nextbiomotif.com
Depends On Me pathview, ROntoTools, SPIA
Imports Me clipper, DEGraph, NCIgraph
Suggests Me DEGraph, GenomicRanges

Package Downloads

Package Source KEGGgraph_1.23.1.tar.gz
Windows Binary KEGGgraph_1.23.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) KEGGgraph_1.23.1.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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