GenomeGraphs

DOI: 10.18129/B9.bioc.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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	The GenomeGraphs users guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Microarray, Software, Visualization
Version	1.46.0
In Bioconductor since	BioC 2.2 (R-2.7) (12 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods, biomaRt, grid
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me	Genominator, waveTiling
Imports Me
Suggests Me	leeBamViews, oligo, oligo
Links To Me
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