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README.md
<img src="vignettes/Gviz-logo.png" align="right" alt="" width="120" /> # _Gviz_ - Plotting data and annotation information along genomic coordinates ## Software status <!-- badges: start --> [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![How long since the package was first in a released Bioconductor version](https://bioconductor.org/shields/years-in-bioc/Gviz.svg)](https://bioconductor.org/packages/Gviz) [![Support site activity in last 6 months: agged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts](https://bioconductor.org/shields/posts/Gviz.svg)](https://support.bioconductor.org/t/gviz/) <!-- badges: end --> | Platform | OS | Last Update | Status | Coverage | Downloads | |:----------|:---------:|:--------------:|:----------------:|:----------------:|:---------:| | Travis CI | Linux | [![GitHub last commit](https://img.shields.io/github/last-commit/ivanek/Gviz)](https://github.com/ivanek/Gviz) | [![Travis CI](https://travis-ci.org/ivanek/Gviz.svg?branch=master)](https://travis-ci.org/ivanek/Gviz) | [![Codecov.io coverage status](https://codecov.io/github/ivanek/Gviz/coverage.svg?branch=master)](https://codecov.io/github/ivanek/Gviz) | NA | | Bioc ([devel](https://bioconductor.org/packages/devel/bioc/html/Gviz.html)) | [![Platforms](https://bioconductor.org/shields/availability/devel/Gviz.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/Gviz/) | [![Bioconductor-devel Last Commit](https://bioconductor.org/shields/lastcommit/devel/bioc/Gviz.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/Gviz/) | [![Bioconductor-devel Build Status](https://bioconductor.org/shields/build/devel/bioc/Gviz.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/Gviz) | NA | [![Bioconductor-devel Downloads](https://bioconductor.org/shields/downloads/devel/Gviz.svg)](https://bioconductor.org/packages/stats/bioc/Gviz/) | | Bioc ([release](https://bioconductor.org/packages/release/bioc/html/Gviz.html)) | [![Platforms](https://bioconductor.org/shields/availability/release/Gviz.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/Gviz/) | [![Bioconductor-release Last Commit](https://bioconductor.org/shields/lastcommit/release/bioc/Gviz.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/Gviz/) | [![Bioconductor-release Build Status](https://bioconductor.org/shields/build/release/bioc/Gviz.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/Gviz) | NA | [![Bioconductor-release Downloads](https://bioconductor.org/shields/downloads/release/Gviz.svg)](https://bioconductor.org/packages/stats/bioc/Gviz/) | <!-- | Travis CI | Linux | [![GitHub last commit](https://img.shields.io/github/last-commit/ivanek/Gviz)](https://github.com/ivanek/Gviz) | [![Travis CI](https://travis-ci.org/ivanek/Gviz.svg?branch=master)](https://travis-ci.org/ivanek/Gviz) | [![Codecov.io coverage status](https://codecov.io/github/ivanek/Gviz/coverage.svg?branch=master)](https://codecov.io/github/ivanek/Gviz) | NA | | Travis CI | Linux | [![GitHub last commit](https://img.shields.io/github/last-commit/ivanek/Gviz)](https://github.com/ivanek/Gviz) | [![Travis CI](https://travis-ci.org/ivanek/Gviz.svg?branch=master)](https://travis-ci.org/ivanek/Gviz) | [![Codecov.io coverage status](https://img.shields.io/codecov/c/github/ivanek/Gviz/master)](https://codecov.io/github/ivanek/Gviz) | NA | --> ## Authors - Florian Hahne - Steffen Durinck - Robert Ivanek - Arne Mueller - Steve Lianoglou - Ge Tan - Lance Parsons - Shraddha Pai ## Overview ![Gviz UCSC like screenshot](vignettes/Gviz-example.png) Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the [biomaRt](https://bioconductor.org/packages/biomaRt/) and the [rtracklayer](https://bioconductor.org/packages/rtracklayer/) packages to perform live annotation queries to [Ensembl](https://www.ensembl.org/) and [UCSC](https://genome.ucsc.edu) 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("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("ivanek/Gviz") ``` ## 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](https://dx.doi.org/10.1007/978-1-4939-3578-9_16).