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JBrowseR

R-CMD-check CRAN status

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:

Live demos

Basic usage including text search index

Allows you to search by gene name

Multi purpose demo app

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

Load config.json file

Shows loading a config.json file

Load data frame

Simple example showing a data frame as a track

Gene fusion example

Shows putative gene fusions in the SKBR3 breast cancer cell line

Using plugins

Uses the config.json loading method

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}
}