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docs: random README fixes
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tuner committed May 6, 2024
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![npm version](https://img.shields.io/npm/v/@genome-spy/core)
[![DOI](https://zenodo.org/badge/153765756.svg)](https://zenodo.org/doi/10.5281/zenodo.7852281)

GenomeSpy is a visualization toolkit for genomic (and other) data. It has a [Vega-Lite](https://vega.github.io/vega-lite/) inspired visualization grammar and a high-performance, WebGL-powered graphics renderer.
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.

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

## Monorepo

GenomeSpy is split into several [packages](./packages/), two (core and app) of which are the most important:
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.
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. A session handling with provenance, url hashes, and bookmarks is included.
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.
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

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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/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.
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`
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

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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/)), Biomedicum Helsinki Foundation, Sigrid
Jusélius Foundation, and the Cancer Foundation Finland.
([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:

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