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GenomeSpy

Teaser

npm version

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

The software is still work in progress. Documentation and examples for the current version can be found at https://genomespy.app/

Monorepo

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

Core

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

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. A session handling with provenance, url hashes, and bookmarks is included.

Contributing

Bootstrapping and running

  1. git clone [email protected]:genome-spy/genome-spy.git
  2. cd genome-spy
  3. npm install (use npm7!)
  4. npm start (starts the App)

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

About

Copyright (c) 2019-2021 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 667403 for HERCULES.

Contains code from: