The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
JBrowseR provides an R interface to the JBrowse 2 genome browser.
JBrowse 2 is “a pluggable open-source platform for visualizing and integrating biological data”. It is a fast and flexible tool that can visualize a wide variety of data. JBrowse 2 was built using powerful modern web technologies such as React and TypeScript. One of the core products of JBrowse 2 is a React component that makes it possible to embed a custom genome browser in a web page.
While the JBrowse 2 component is an incredible tool, the main way for developers to use it has been to add it to a React app, which comes with a steep learning curve. That is where JBrowseR comes in! Using JBrowseR, it is now possible to:
And it is possible to do this writing only a small amount of R code.
The core function of the package is JBrowseR(). There
are two key arguments:
There are a lot of possibilities with all of these options! So let’s start simple. The interface enables a progressive disclosure of complexity.
The only necessary argument is which view. To launch a hg19 browser from the console run:
JBrowseR("ViewHg19")The ViewHg19 and ViewHg38 views are the
simplest components of the package. They return pre-configured browsers
displaying the reference assembly and NCBI RefSeq annotations of the
hg19 and hg38 genomes respectively.
We can extend the example to see how optional arguments work by setting the location:
JBrowseR("ViewHg19",
location = "10:29,838,737..29,838,819")This will set the starting location of the browser when it is first loaded.
While the hg19 and hg38 views can be great tools for quickly
launching a browser, we have already reached the end of the road for
what can be done with them. The main interface of this package involves
using the more general View component. For a tutorial
showing how to create a small Shiny application with custom data tracks,
head to:
Although the View components provides fairly exhaustive
access to the customization options of JBrowse 2, it does not expose all
of the options available. If you find yourself wanting to use advanced
features such as coloring features with JavaScript callbacks, or to use
more specific rendering functions, it is possible to use the
JsonView to use a JSON configured browser. This provides
full access to the configuration API available for JavaScript users of
JBrowse 2. For a tutorial on what this looks like, visit:
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.