output: github_document

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

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

Live demos

Basic usage including text search index

Allows you to search by gene name

• Link demo: https://gmod.shinyapps.io/basic_usage_with_text_index
• Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/basic_usage_with_text_index/app.R

Multi purpose demo app

Shows a "bookmark" type feature, loading data from data frame, and buttons to navigate to genes of interest

• Live link: https://gmod.shinyapps.io/bookmarks_demo
• Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/bookmarks_demo/app.R

Load config.json file

Shows loading a config.json file

• Live link: https://gmod.shinyapps.io/load_config_json
• Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/load_config_json/app.R

Load data frame

Simple example showing a data frame as a track

• Live link: https://gmod.shinyapps.io/load_data_frame
• Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/load_data_frame/app.R

Gene fusion example

Shows putative gene fusions in the SKBR3 breast cancer cell line

• Live link: https://gmod.shinyapps.io/skbr3_gene_fusions
• Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/skbr3_gene_fusions/app.R

Using plugins

Uses the config.json loading method

• Live link: not yet online
• Source code: https://github.com/GMOD/JBrowseR/blob/main/example_apps/using_plugins/app.R

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}
}