KEGGgraph
This is the development version of KEGGgraph; for the stable release version, see KEGGgraph.
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
Bioconductor version: Development (3.24)
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 roche.com>
citation("KEGGgraph")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("KEGGgraph")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("KEGGgraph")| KEGGgraph: Application Examples | R Script | |
| KEGGgraph: graph approach to KEGG PATHWAY | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, KEGG, Pathways, Software, Visualization |
| Version | 1.73.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (17.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5.0) |
| Imports | methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz |
| System Requirements | |
| URL | https://accio.github.io/research/#software |
See More
| Suggests | RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA |
| Linking To | |
| Enhances | |
| Depends On Me | lpNet, ROntoTools, SPIA |
| Imports Me | clipper, DEGraph, EnrichmentBrowser, MetaboSignal, MWASTools, NCIgraph, pathview |
| Suggests Me | DEGraph, GenomicRanges, kangar00, maGUI, rags2ridges, specmine |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | KEGGgraph_1.73.0.tar.gz |
| Windows Binary (x86_64) | KEGGgraph_1.73.0.zip |
| macOS Binary (big-sur-x86_64) | KEGGgraph_1.73.0.tgz |
| macOS Binary (sonoma-arm64) | KEGGgraph_1.73.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/KEGGgraph |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/KEGGgraph |
| Bioc Package Browser | https://code.bioconductor.org/browse/KEGGgraph/ |
| Package Short Url | https://bioconductor.org/packages/KEGGgraph/ |
| Package Downloads Report | Download Stats |