biocGraph
This is the released version of biocGraph; for the devel version, see biocGraph.
Graph examples and use cases in Bioinformatics
Bioconductor version: Release (3.23)
This package provides examples and code that make use of the different graph related packages produced by Bioconductor.
Author: Li Long <li.long at isb-sib.ch>, Robert Gentleman <rgentlem at fhcrc.org>, Seth Falcon <sethf at fhcrc.org> Florian Hahne <fhahne at fhcrc.org>
Maintainer: Florian Hahne <florian.hahne at novartis.com>
citation("biocGraph")):
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")
BiocManager::install("biocGraph")
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("biocGraph")| Examples of plotting graphs Using Rgraphviz | R Script | |
| HOWTO layout pathways | R Script | |
| Reference Manual |
Details
| biocViews | GraphAndNetwork, Software, Visualization |
| Version | 1.74.0 |
| In Bioconductor since | BioC 2.1 (R-2.6) (19 years) |
| License | Artistic-2.0 |
| Depends | Rgraphviz, graph |
| Imports | Rgraphviz, geneplotter, graph, BiocGenerics, methods |
| System Requirements | |
| URL |
See More
| Suggests | fibroEset, geneplotter, hgu95av2.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | EnrichmentBrowser |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | biocGraph_1.74.0.tar.gz |
| Windows Binary (x86_64) | biocGraph_1.74.0.zip |
| macOS Binary (big-sur-x86_64) | biocGraph_1.74.0.tgz |
| macOS Binary (sonoma-arm64) | biocGraph_1.74.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/biocGraph |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/biocGraph |
| Bioc Package Browser | https://code.bioconductor.org/browse/biocGraph/ |
| Package Short Url | https://bioconductor.org/packages/biocGraph/ |
| Package Downloads Report | Download Stats |