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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("KEGGgraph")
In most cases, you don't need to download the package archive at all.
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:
source("http://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) |
| 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 |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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