https://github.com/higlass/higlass
Fast, flexible and extensible genome browser.
https://github.com/higlass/higlass
gehlenborglab genomics hi-c higlass visualization
Last synced: 5 months ago
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Fast, flexible and extensible genome browser.
- Host: GitHub
- URL: https://github.com/higlass/higlass
- Owner: higlass
- License: mit
- Created: 2016-04-12T02:58:30.000Z (over 9 years ago)
- Default Branch: develop
- Last Pushed: 2025-03-18T00:37:28.000Z (7 months ago)
- Last Synced: 2025-04-03T03:39:21.550Z (6 months ago)
- Topics: gehlenborglab, genomics, hi-c, higlass, visualization
- Language: JavaScript
- Homepage: http://higlass.io
- Size: 154 MB
- Stars: 320
- Watchers: 20
- Forks: 52
- Open Issues: 31
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.bib
Awesome Lists containing this project
README
[](https://docs.higlass.io/)
[](https://zenodo.org/badge/latestdoi/56026057)
[](https://twitter.com/higlass_io)
[](https://tinyurl.com/3z3bds4w)
### Introduction
HiGlass is a web-based viewer for datasets too large to view at once. It
features synchronized navigation of multiple views as well as continuous
zooming and panning for navigation across genomic loci and resolutions. It
supports visual comparison of genomic (e.g., Hi-C, ChIP-seq, or bed
annotations) and other data (e.g., geographic maps, gigapixel images, or
abstract 1D and 2D sequential 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 [https://higlass.io](https://higlass.io). A
[Docker container](https://github.com/higlass/higlass-docker) is available for
running an instance locally, although we recommend using the
[higlass-manage](https://github.com/pkerpedjiev/higlass-manage) package to
start, stop and configure local instances.
For documentation about how to use and install HiGlass, please visit
[https://docs.higlass.io](https://docs.higlass.io).
### Citation
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
### Example
### Development
To run higlass from its source code simply run the following:
```
npm clean-install // use --legacy-peer-deps if you get peer dependency errors
npm start
```
This starts a server in development mode at http://localhost:5173/.
> **Warning**
> The following examples need to be migrated to the latest build.
> Once started, a list of the examples can be found at [http://localhost:8080/examples.html](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](http://localhost:8080/apis/svg.html?/viewconfs/overlay-tracks.json).
### Tests
The tests for the React components and API functions are located in the `test`
directory. Tests are run with [`vitest`](https://vitest.dev/).
Useful commands:
- Run all tests in the browser: `npm test -- --browser.headless=false`
See the [contributing guide](./CONTRIBUTING.md) to learn more.
### API
HiGlass provides an API for controlling the component from with JavaScript. Below is a [minimal working example](docs/examples/others/minimal-working-example.html) to get started and the complete documentation is availabe at [docs.higlass.io](http://docs.higlass.io/javascript_api.html).
```html
Minimal Working Example · HiGlass
html, body {
width: 100vw;
height: 100vh;
overflow: hidden;
}
import * as hglib from "https://esm.sh/higlass@1.13";
const api = hglib.viewer(
document.body,
'https://higlass.io/api/v1/viewconfs/?d=default',
{ bounded: true },
);