Gviz
This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.
Install / Use
/learn @ivanek/GvizREADME
Gviz - Plotting data and annotation information along genomic coordinates
Software status
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Authors
- Florian Hahne
- Steffen Durinck
- Robert Ivanek
- Arne Mueller
- Steve Lianoglou
- Ge Tan
- Lance Parsons
- Shraddha Pai
Overview
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC 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.
Installation
Release version
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Gviz", version = "release")
Developmental version
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Gviz", version = "devel")
Github
if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("ivanek/Gviz")
Usage
For detailed instructions check the package vignette (release or developmental version). Or check the GitHub.io page.
Citation
- Hahne F, Ivanek R (2016). "Statistical Genomics: Methods and Protocols." In Mathé E, Davis S (eds.), chapter Visualizing Genomic Data Using Gviz and Bioconductor, 335–351. Springer New York, New York, NY. ISBN 978-1-4939-3578-9, doi: 10.1007/978-1-4939-3578-9_16.
