HiGlass is a web-based viewer for genome interaction maps featuring synchronized navigation of multiple views as well as continuous zooming and panning for navigation across genomic loci and resolutions. It supports visual comparison of Hi-C and other genomic data from different experimental conditions and can be used to efficiently identify salient outcomes of experimental perturbations, generate new hypotheses, and share the results with the community.
A live instance can be found at http://higlass.io. A Docker container is available for running an instance locally, although we recommend using the higlass-manage package to start, stop and configure local instances.
For documentation about how to use and install HiGlass, please visit http://docs.higlass.io.
Kerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., ... & Gehlenborg, N. HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps. Genome Biology (2018): 19:125. https://doi.org/10.1186/s13059-018-1486-1
To run higlass from its source code simply run the following:
npm install
npm run start
This starts a server in development mode at http://localhost:8080/.
Once started, a list of the examples can be found at http://localhost:8080/examples.html.
Template viewconfs located at /docs/examples/viewconfs can viewed directly at urls such as http://localhost:8080/apis/svg.html?/viewconfs/overlay-tracks.json.
The tests for the React components and API functions are located in the test directory. To save time and only run relevant tests, open karma.conf.js and select the test files to run before running test-watch.
npm run test-watch
Troubleshooting:
-
If the installation fails due to
sharp>node-gyptry installing the node packages usingpython2:npm i --python=/usr/bin/python2 && rm -rf node_modules/node-sass && npm i
HiGlass provides an API for controlling the component from within a Javascript script. Complete documentation is availabe at docs.higlass.io. Example:
<link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" type="text/css">
<link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/styles/hglib.css" type="text/css">
<script src="https://cdnjs.cloudflare.com/ajax/libs/react/15.6.2/react.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/react-dom/15.6.2/react-dom.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/pixi.js/4.6.2/pixi.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/react-bootstrap/0.31.0/react-bootstrap.min.js"></script>
<script src="https://unpkg.com/[email protected]/dist/scripts/hglib.js"></script>
<div
id="development-demo"
style="position: absolute; left: 1rem; top: 1rem; bottom: 1rem; right: 1rem">
</div>
<script>
const api = hglib.createHgComponent(
document.getElementById('development-demo'),
'http://higlass.io/api/v1/viewconfs/?d=default',
{ bounded: true }
);
</script>
- HiGlass Manage - Easy to use interface for deploying a local HiGlass instance
- HiGlass Docker - Build an image containing all the components necessary to deploy HiGlass
- HiGlass Server - Server component for serving multi-resolution data
- HiGlass App - The code for the web application hosted at http://higlass.io
HiGlass is provided under the MIT License.