GenomeGraphs
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GenomeGraphs.
Plotting genomic information from Ensembl
Bioconductor version: 3.10
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.
Author: Steffen Durinck <sdurinck at gmail.com>, James Bullard <bullard at berkeley.edu>
Maintainer: Steffen Durinck <sdurinck at gmail.com>
citation("GenomeGraphs")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomeGraphs")
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("GenomeGraphs")| The GenomeGraphs users guide | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microarray, Software, Visualization |
| Version | 1.46.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) (16 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), methods, biomaRt, grid |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | Genominator, waveTiling |
| Imports Me | |
| Suggests Me | leeBamViews, oligo, oligo |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomeGraphs_1.46.0.tar.gz |
| Windows Binary | GenomeGraphs_1.46.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | GenomeGraphs_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomeGraphs |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomeGraphs |
| Package Short Url | https://bioconductor.org/packages/GenomeGraphs/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |