KEGGgraph

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

Bioconductor version: 2.7

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 and Stefan Wiemann

Maintainer: Jitao David Zhang <j.zhang at dkfz.de>

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

Details

biocViews Pathways, GraphsAndNetworks
Depends methods, XML (>= 2.3-0), graph, Rgraphviz(>= 1.22.0)
Imports methods, XML, graph
Suggests RBGL, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA
System Requirements
License GPL (>= 2)
URL http://www.dkfz.de/en/mga/index.html
Depends On Me
Imports Me DEGraph
Suggests Me DEGraph, SPIA
Version 1.6.0
Since Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source KEGGgraph_1.6.0.tar.gz
Windows Binary KEGGgraph_1.6.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary KEGGgraph_1.6.0.tgz
Package Downloads Report Download Stats

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