KEGGgraph

"KEGGgraph" is a software package that facilitates integrating and analyzing KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways through graph theory. KEGG PATHWAY, a service provided by KEGG, offers manually curated pathway maps that represent the current understanding of biological networks using graph models. Despite the value of these pathways, there has been a gap in tools capable of parsing and analyzing them with graph theory.

KEGGgraph addresses this gap by providing an interface between KEGG pathways and graph models alongside a suite of tools for graph analysis. This package captures the complex topology of pathways, allowing users to conduct detailed analyses or dissect pathway graphs for further study.

Topic

Molecular interactions, pathways and networks;Data visualisation

Detail

  • Operation: Pathway or network analysis;Visualisation

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.62.0

  • Credit: National Genome Research Network of the German Federal Ministry of Education and Research (BMBF).

  • Input: -

  • Output: -

  • Contact: Jitao David Zhang jitao_david.zhang@roche.com

  • Collection: -

  • Maturity: Stable

Publications

  • KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.
  • Zhang JD and Wiemann S. KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. 2009; 25:1470-1. doi: 10.1093/bioinformatics/btp167
  • https://doi.org/10.1093/bioinformatics/btp167
  • PMID: 19307239
  • PMC: PMC2682514

Download and documentation

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