DOI: 10.18129/B9.bioc.KEGGgraph  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see KEGGgraph.

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

Bioconductor version: 3.16

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>

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


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


biocViews GraphAndNetwork, KEGG, Pathways, Software, Visualization
Version 1.58.3
In Bioconductor since BioC 2.4 (R-2.9) (14 years)
License GPL (>= 2)
Depends R (>= 3.5.0)
Imports methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz
Suggests RBGL, testthat, RColorBrewer,, hgu133plus2.db, SPIA
Depends On Me ROntoTools, SPIA
Imports Me clipper, DEGraph, EnrichmentBrowser, KEGGlincs, MetaboSignal, MWASTools, NCIgraph, pathview, PFP
Suggests Me DEGraph, GenomicRanges
Links To Me
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