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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
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KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
Bioconductor version: Release (3.5)
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, KEGG, Pathways, Software, Visualization |
| Version | 1.38.1 |
| In Bioconductor since | BioC 2.4 (R-2.9) (8.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0) |
| Imports | methods, XML (>= 2.3-0), graph, utils |
| 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 | ROntoTools, SPIA |
| Imports Me | clipper, DEGraph, EnrichmentBrowser, KEGGlincs, MetaboSignal, NCIgraph, pathview, ToPASeq |
| Suggests Me | DEGraph, GenomicRanges |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | KEGGgraph_1.38.1.tar.gz |
| Windows Binary | KEGGgraph_1.38.1.zip |
| Mac OS X 10.11 (El Capitan) | KEGGgraph_1.38.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/KEGGgraph |
| Package Short Url | http://bioconductor.org/packages/KEGGgraph/ |
| Package Downloads Report | Download Stats |
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