https://github.com/genome-spy/genome-spy
A visualization grammar and GPU-accelerated toolkit for genomic data
https://github.com/genome-spy/genome-spy
bioinformatics cancer-genomics data-visualization genome genome-visualization graphics visual-analytics visualization webgl
Last synced: 6 months ago
JSON representation
A visualization grammar and GPU-accelerated toolkit for genomic data
- Host: GitHub
- URL: https://github.com/genome-spy/genome-spy
- Owner: genome-spy
- License: mit
- Created: 2018-10-19T10:24:48.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2026-01-16T07:56:54.000Z (6 months ago)
- Last Synced: 2026-01-17T07:30:42.125Z (6 months ago)
- Topics: bioinformatics, cancer-genomics, data-visualization, genome, genome-visualization, graphics, visual-analytics, visualization, webgl
- Language: JavaScript
- Homepage: http://genomespy.app/
- Size: 13.5 MB
- Stars: 188
- Watchers: 4
- Forks: 11
- Open Issues: 80
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
- Agents: AGENTS.md
Awesome Lists containing this project
- awesome-web-visualization-frameworks - genome-spy - WebGL based datavis with scales and zoom. (Uncategorized / Uncategorized)
README
# GenomeSpy
[](https://zenodo.org/doi/10.5281/zenodo.7852281)
GenomeSpy is a visualization toolkit for genomic (and other) data. It features a
visualization grammar inspired by [Vega-Lite](https://vega.github.io/vega-lite/)
and a high-performance, WebGL-powered graphics renderer.
Documentation and examples can be found at https://genomespy.app/
## Monorepo
GenomeSpy is split into several [packages](./packages/), two of which, core and
app, are the most important:
### Core
The [core](./packages/core/) library provides the visualization grammar and a
WebGL-powered rendering engine.
### Cohort App
The [app](./packages/app/) builds upon the core, extending the visualization
grammar with support for faceting multiple (up to thousands of) patient samples.
It provides a user interface for interactive analysis of the samples, which can
be filtered, sorted, and grouped flexibly. The app includes session handling
with provenance, URL hashes, and bookmarks.
### Embed Examples
The [embed-examples](./packages/embed-examples/) package contains examples of
how to embed GenomeSpy in web applications and use the
[API](https://genomespy.app/docs/api/) for advanced use cases.
## Contributing
### Bootstrapping and running
1. `git clone git@github.com:genome-spy/genome-spy.git`
2. `cd genome-spy`
3. `npm install` (use npm7!)
4. `npm start` (starts a development server with the app package)
The `packages/core/examples` directory contains some random view specification
that can be accessed through urls like
`http://localhost:8080/?spec=examples/first.json`.
The `packages/core/private/` directory is in `.gitignore` and served by the
development server: `http://localhost:8080/?spec=private/foo.json`. Use it for
experiments that should not go into version control.
If you want to use or develop the core library, launch a single-page app using:
`npm -w @genome-spy/core run dev`
### Contributing guidelines
Please see the [CONTRIBUTING.md](./CONTRIBUTING.md) file for more information.
## Citing
If you use GenomeSpy in your research, please cite the following paper:
Kari Lavikka, Jaana Oikkonen, Yilin Li, Taru Muranen, Giulia Micoli, Giovanni
Marchi, Alexandra Lahtinen, Kaisa Huhtinen, Rainer Lehtonen, Sakari Hietanen,
Johanna Hynninen, Anni Virtanen, Sampsa Hautaniemi, Deciphering cancer genomes
with GenomeSpy: a grammar-based visualization toolkit, _GigaScience_, Volume 13,
2024, giae040, https://doi.org/10.1093/gigascience/giae040
## About
Copyright (c) 2019-2024 Kari Lavikka. See [LICENSE](LICENSE) for details.
GenomeSpy is developed in [The Systems Biology of Drug Resistance in
Cancer](https://www.helsinki.fi/en/researchgroups/systems-biology-of-drug-resistance-in-cancer)
group at the [University of Helsinki](https://www.helsinki.fi/en).
This project has received funding from the European Union's Horizon 2020
research and innovation programme under grant agreement No. 965193
([DECIDER](https://www.deciderproject.eu/)) and No. 847912
([RESCUER](https://www.rescuer.uio.no/)), as well as from the Biomedicum
Helsinki Foundation, the Sigrid Jusélius Foundation, and the Cancer Foundation
Finland.
Contains some code copied and adapted from the following projects:
- Vega and Vega-Lite ([LICENSE](https://github.com/vega/vega-lite/blob/master/LICENSE))
- TWGL ([LICENSE](https://github.com/greggman/twgl.js/blob/master/LICENSE.md))