- Home
- Bioconductor 3.0
- Software Packages
- KEGGgraph
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("KEGGgraph")
In most cases, you don't need to download the package archive at all.
KEGGgraph
|
This package is for version 3.0 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: 3.0
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>
Citation (from within R,
enter citation("KEGGgraph")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("KEGGgraph")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("KEGGgraph")
| R Script | KEGGgraph: Application Examples | |
| R Script | KEGGgraph: graph approach to KEGG PATHWAY | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GraphAndNetwork, Pathways, Software, Visualization |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (7 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10), methods, XML (>= 2.3-0), graph |
| Imports | methods, XML, graph |
| LinkingTo | |
| Suggests | Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA |
| SystemRequirements | |
| Enhances | |
| URL | http://www.nextbiomotif.com |
| Depends On Me | EnrichmentBrowser, pathview, ROntoTools, SPIA |
| Imports Me | clipper, DEGraph, NCIgraph |
| Suggests Me | DEGraph, GenomicRanges |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | KEGGgraph_1.24.0.tar.gz |
| Windows Binary | KEGGgraph_1.24.0.zip |
| Mac OS X 10.6 (Snow Leopard) | KEGGgraph_1.24.0.tgz |
| Mac OS X 10.9 (Mavericks) | KEGGgraph_1.24.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/KEGGgraph/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/KEGGgraph/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
