KEGGgraph

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

Bioconductor version: 2.10

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

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 GraphsAndNetworks, Pathways, Software
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
License GPL (>= 2)
URL http://www.nextbiomotif.com
Depends On Me
Imports Me DEGraph, NCIgraph
Suggests Me DEGraph, SPIA
Version 1.12.0
Since Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source KEGGgraph_1.12.0.tar.gz
Windows Binary KEGGgraph_1.12.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary KEGGgraph_1.12.0.tgz
Package Downloads Report Download Stats

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