Gviz - Plotting data and annotation information along genomic coordinates

Software status

 

Bioc (release) Bioc (devel)
OS Platforms Platforms
Bioc Last Update Bioconductor-release Last Commit Bioconductor-devel Last Commit
Bioc Status Bioconductor-release Build Status Bioconductor-devel Build Status
GitHub Last Commit GitHub last commit (Bioconductor-release) GitHub last commit (Bioconductor-devel)
GitHub Actions R build status R build status
Coverage Codecov.io (Bioconductor-release) Codecov.io (Bioconductor-devel)

Authors

  • Florian Hahne
  • Steffen Durinck
  • Robert Ivanek
  • Arne Mueller
  • Steve Lianoglou
  • Ge Tan
  • Lance Parsons
  • Shraddha Pai

Overview

Gviz UCSC like screenshot
Gviz UCSC like screenshot

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.