genome-spy
A visualization grammar and GPU-accelerated toolkit for genomic data
Science Score: 67.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
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○Scientific vocabulary similarity
Low similarity (15.6%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A visualization grammar and GPU-accelerated toolkit for genomic data
Basic Info
- Host: GitHub
- Owner: genome-spy
- License: mit
- Language: JavaScript
- Default Branch: master
- Homepage: http://genomespy.app/
- Size: 14.4 MB
Statistics
- Stars: 183
- Watchers: 4
- Forks: 11
- Open Issues: 75
- Releases: 101
Topics
Metadata Files
README.md
GenomeSpy
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/
Monorepo
GenomeSpy is split into several packages, two of which, core and app, are the most important:
Core
The core library provides the visualization grammar and a WebGL-powered rendering engine.
Cohort App
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.
Embed Examples
The embed-examples package contains examples of how to embed GenomeSpy in web applications and use the API for advanced use cases.
Contributing
Bootstrapping and running
git clone git@github.com:genome-spy/genome-spy.gitcd genome-spynpm install(use npm7!)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 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 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 Juslius Foundation, and the Cancer Foundation Finland.
Contains some code copied and adapted from the following projects:
Owner
- Name: GenomeSpy
- Login: genome-spy
- Kind: organization
- Location: Finland
- Website: https://genomespy.app/
- Repositories: 2
- Profile: https://github.com/genome-spy
A GPU-powered visualization toolkit for genomic and other data
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: GenomeSpy
message: >-
If you use this software in your research, please
cite it as below.
type: software
authors:
- given-names: Kari
family-names: Lavikka
email: kari.lavikka@helsinki.fi
affiliation: University of Helsinki
orcid: 'https://orcid.org/0000-0002-4163-4945'
url: "https://genomespy.app/"
GitHub Events
Total
- Create event: 14
- Issues event: 18
- Release event: 8
- Watch event: 7
- Delete event: 4
- Issue comment event: 5
- Push event: 46
- Pull request review event: 2
- Pull request review comment event: 3
- Pull request event: 7
- Fork event: 2
Last Year
- Create event: 14
- Issues event: 18
- Release event: 8
- Watch event: 7
- Delete event: 4
- Issue comment event: 5
- Push event: 46
- Pull request review event: 2
- Pull request review comment event: 3
- Pull request event: 7
- Fork event: 2
Committers
Last synced: 6 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Kari Lavikka | k****a@h****i | 1,873 |
| dependabot[bot] | 4****] | 4 |
| Lavikka | k****a@l****l | 2 |
| trentfridey | t****2@g****m | 1 |
| Lavikka | k****a@l****i | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 157
- Total pull requests: 81
- Average time to close issues: 7 months
- Average time to close pull requests: about 1 month
- Total issue authors: 6
- Total pull request authors: 4
- Average comments per issue: 0.63
- Average comments per pull request: 0.3
- Merged pull requests: 54
- Bot issues: 0
- Bot pull requests: 22
Past Year
- Issues: 13
- Pull requests: 17
- Average time to close issues: 29 days
- Average time to close pull requests: 2 days
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.06
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 7
Top Authors
Issue Authors
- tuner (148)
- mattjvincent (3)
- EddyGenome (2)
- razsultana (2)
- slobentanzer (1)
- okunator (1)
Pull Request Authors
- tuner (63)
- dependabot[bot] (31)
- razsultana (2)
- trentfridey (2)
Top Labels
Issue Labels
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Dependencies
- 904 dependencies
- @commitlint/cli ^16.2.4 development
- @commitlint/config-conventional ^16.2.4 development
- eslint ^8.1.0 development
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- husky ^8.0.1 development
- lerna ^4.0.0 development
- lint-staged ^12.4.1 development
- node-sass ^7.0.1 development
- prettier ^2.5.1 development
- pretty-quick ^3.1.3 development
- regenerator-runtime ^0.13.9 development
- rollup-plugin-glsl ^1.3.0 development
- rollup-plugin-minify-html-literals ^1.2.6 development
- sass ^1.49.7 development
- ts-json-schema-generator ^1.0.0 development
- typescript ^4.6.0-dev.20211122 development
- vite ^2.8.0 development
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- @fortawesome/fontawesome-free ^6.1.1
- @fortawesome/fontawesome-svg-core ^6.1.1
- @fortawesome/free-solid-svg-icons ^6.1.1
- @genome-spy/core ^0.22.1
- @reduxjs/toolkit ^1.6.2
- idb ^7.0.1
- lit ^2.0.2
- lz-string ^1.4.4
- mapsort ^1.0.5
- redux-batched-actions ^0.5.0
- redux-undo ^1.0.1
- snarkdown ^2.0.0
- @types/d3-array ^3.0.2
- @types/d3-dsv ^3.0.0
- @types/d3-ease ^3.0.0
- @types/d3-format ^3.0.1
- @types/d3-interpolate ^3.0.1
- @types/d3-scale ^4.0.2
- d3-array ^3.1.1
- d3-color ^3.0.1
- d3-ease ^3.0.1
- d3-format ^3.0.1
- flatqueue ^2.0.3
- internmap ^2.0.3
- lit-html ^2.0.2
- twgl.js ^4.19.1
- vega-expression ^5.0.0
- vega-loader ^4.4.0
- vega-scale ^7.1.1
- vega-util ^1.16.0
- @genome-spy/core ^0.22.1
- lit ^2.0.0-rc.2
- @genome-spy/core ^0.22.1
- lit ^2.0.0-rc.2
- @fortawesome/fontawesome-free ^6.1.1
- @fortawesome/fontawesome-svg-core ^6.1.1
- @fortawesome/free-solid-svg-icons ^6.1.1
- @genome-spy/core ^0.22.1
- lit ^2.0.2
- monaco-editor ^0.30.1
- vega-loader ^4.4.0
- actions/checkout v2 composite
- actions/setup-node v2 composite
- actions/setup-python v2 composite
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- actions/checkout v2 composite
- actions/setup-node v2 composite