JBrowseR

JBrowseR is an R package that provides a simple and clean interface to JBrowse 2 for R users. Using JBrowseR, you can:

• Embed the JBrowse 2 genome browser in R Markdown documents and Shiny applications
• Deploy a genome browser directly from the R console to view your data
• Customize your genome browser to display your own data

With this functionality, you can deploy a first-class genome browser with your data in just a few lines of R code!

Installation

You can install the released version of JBrowseR from CRAN with:

install.packages("JBrowseR")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("gmod/JBrowseR")

Example

This line of code can be used to launch a genome browser from your R console:

library(JBrowseR)
JBrowseR("ViewHg19",
         location = "10:29,838,737..29,838,819")

Getting started

In order to get started with JBrowseR, please refer to the vignette that best suits your needs:

• Introduction
• Custom browser tutorial
• JSON configuration tutorial
• Creating URLS

Citation

If you use JBrowseR in your research, please cite the following publication:

Hershberg et al., 2021. JBrowseR: An R Interface to the JBrowse 2 Genome Browser

@article{hershberg2021jbrowser,
  title={JBrowseR: An R Interface to the JBrowse 2 Genome Browser},
  author={Hershberg, Elliot A and Stevens, Garrett and Diesh, Colin and Xie, Peter and De Jesus Martinez, Teresa and Buels, Robert and Stein, Lincoln and Holmes, Ian},
  journal={Bioinformatics}
}