Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
9 of 34 committers (26.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.8%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Fast, flexible and extensible genome browser.
Basic Info
- Host: GitHub
- Owner: higlass
- License: mit
- Language: JavaScript
- Default Branch: main
- Homepage: http://higlass.io
- Size: 154 MB
Statistics
- Stars: 332
- Watchers: 20
- Forks: 52
- Open Issues: 40
- Releases: 234
Topics
Metadata Files
README.md
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. 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 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. Template viewconfs located at
/docs/examples/viewconfscan viewed directly at urls such as 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.
Useful commands:
- Run all tests in the browser:
npm test -- --browser.headless=false
See the contributing guide to learn more.
API
HiGlass provides an API for controlling the component from with JavaScript. Below is a minimal working example to get started and the complete documentation is availabe at docs.higlass.io.
```html <!DOCTYPE html>