README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# JBrowseR <img src='man/figures/logo.png' align="right" height="136" />

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JBrowseR is an R package that provides a simple and clean interface to [JBrowse 2](https://jbrowse.org/jb2/) 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 **soon** install the released version of JBrowseR from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("JBrowseR")
```

And the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("elliothershberg/JBrowseR")
```
## Example

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

```{r example, eval=FALSE}
library(JBrowseR)
JBrowseR("ViewHg19",
         location = "10:29,838,737..29,838,819")
```

<img src="man/figures/README-example-1.png" width="100%" />

## Getting started

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

- [Introduction](https://elliothershberg.github.io/JBrowseR/articles/JBrowseR.html)
- [Custom browser tutorial](https://elliothershberg.github.io/JBrowseR/articles/custom-browser-tutorial.html)
- [JSON configuration tutorial](https://elliothershberg.github.io/JBrowseR/articles/json-tutorial.html)
- [Creating URLS](https://elliothershberg.github.io/JBrowseR/articles/creating-urls.html)