GenomeSpy is a visualization toolkit for genomic (and other) data. It features a visualization grammar inspired by Vega-Lite and a high-performance, WebGL-powered graphics renderer.

Documentation and examples can be found at https://genomespy.app/

GenomeSpy is split into several packages, two of which, core and app, are the most important:

The core library provides the visualization grammar and a WebGL-powered rendering engine.

The 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.

The embed-examples package contains examples of how to embed GenomeSpy in web applications and use the API for advanced use cases.

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

Please see the CONTRIBUTING.md file for more information.

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

Copyright (c) 2019-2024 Kari Lavikka. See LICENSE for details.

GenomeSpy is developed in The Systems Biology of Drug Resistance in Cancer group at the University of Helsinki.

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 965193 (DECIDER) and No. 847912 (RESCUER), 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)
• TWGL (LICENSE)