<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) [![Bioconductor-devel Downloads](https://bioconductor.org/shields/downloads/devel/Gviz.svg)](https://bioconductor.org/packages/stats/bioc/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/) [![License: Artistic-2.0](https://img.shields.io/badge/License-Artistic%202.0-0298c3.svg)](https://opensource.org/licenses/Artistic-2.0) [![GitHub issues](https://img.shields.io/github/issues/ivanek/Gviz)](https://github.com/ivanek/Gviz/issues) <!-- badges: end --> &nbsp; | | Bioc ([release](https://bioconductor.org/packages/release/bioc/html/Gviz.html)) | Bioc ([devel](https://bioconductor.org/packages/devel/bioc/html/Gviz.html)) | |:--------------------|----------------------------------------------------------------------------:|--------------------------------------------------------------------------------:| | OS | [![Platforms](https://bioconductor.org/shields/availability/release/Gviz.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/Gviz/) | [![Platforms](https://bioconductor.org/shields/availability/devel/Gviz.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/Gviz/) | | Bioc Last Update | [![Bioconductor-release Last Commit](https://bioconductor.org/shields/lastcommit/release/bioc/Gviz.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/Gviz/) | [![Bioconductor-devel Last Commit](https://bioconductor.org/shields/lastcommit/devel/bioc/Gviz.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/Gviz/) | | Bioc Status | [![Bioconductor-release Build Status](https://bioconductor.org/shields/build/release/bioc/Gviz.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/Gviz) | [![Bioconductor-devel Build Status](https://bioconductor.org/shields/build/devel/bioc/Gviz.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/Gviz) | | GitHub Last Commit | [![GitHub last commit (Bioconductor-release)](https://img.shields.io/github/last-commit/ivanek/Gviz/RELEASE_3_14)](https://github.com/ivanek/Gviz/tree/RELEASE_3_14) | [![GitHub last commit (Bioconductor-devel)](https://img.shields.io/github/last-commit/ivanek/Gviz/master)](https://github.com/ivanek/Gviz/tree/master/) | | GitHub Actions | [![R build status](https://github.com/ivanek/Gviz/workflows/R-CMD-check-bioc/badge.svg?branch=RELEASE_3_14)](https://github.com/ivanek/Gviz/actions) | [![R build status](https://github.com/ivanek/Gviz/workflows/R-CMD-check-bioc/badge.svg?branch=master)](https://github.com/ivanek/Gviz/actions) | | Coverage | [![Codecov.io (Bioconductor-release)](https://codecov.io/github/ivanek/Gviz/coverage.svg?branch=RELEASE_3_14)](https://codecov.io/gh/ivanek/Gviz/branch/RELEASE_3_14) | [![Codecov.io (Bioconductor-devel)](https://codecov.io/github/ivanek/Gviz/coverage.svg?branch=master)](https://codecov.io/github/ivanek/Gviz) | ## 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("remotes", quietly = TRUE)) install.packages("remotes") remotes::install_github("ivanek/Gviz") ``` ## Usage For detailed instructions check the package vignette ([release](https://bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.html) or [developmental](https://bioconductor.org/packages/devel/bioc/vignettes/Gviz/inst/doc/Gviz.html) version). Or check the [GitHub.io page](https://ivanek.github.io/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).