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Kerpedjiev","email":"pkerpedjiev@gmail.com"},"license":"MIT","homepage":"https://github.com/alexpreynolds/higlass#readme","keywords":["hi-c","genomics","matrix","tracks"],"repository":{"type":"git","url":"git+https://github.com/alexpreynolds/higlass.git"},"description":"HiGlass Hi-C / genomic / large data viewer","maintainers":[{"name":"apr144","email":"alexpreynolds@gmail.com"}],"readme":"![Build Status](https://github.com/higlass/higlass/actions/workflows/ci.yml/badge.svg)\n[![Live Docs](https://img.shields.io/badge/docs-live-red.svg?colorB=0f9256)](https://docs.higlass.io/)\n[![DOI](https://zenodo.org/badge/56026057.svg)](https://zenodo.org/badge/latestdoi/56026057)\n[![Twitter](https://img.shields.io/badge/news-twitter-red.svg?colorB=6930bf)](https://twitter.com/higlass_io)\n[![Slack](https://img.shields.io/badge/join-Slack-red.svg?colorB=ff4000)](https://tinyurl.com/3z3bds4w)\n\n\n### Introduction\n\nHiGlass is a web-based viewer for datasets too large to view at once.\nIt features synchronized navigation of multiple views as well as continuous zooming and panning\nfor navigation across genomic loci and resolutions. It supports visual comparison of\ngenomic (e.g., Hi-C, ChIP-seq, or bed annotations) and other data (e.g., geographic maps, gigapixel images, or abstract 1D and 2D sequential data) from different experimental conditions and can be used to efficiently\nidentify salient outcomes of experimental perturbations, generate new hypotheses, and share\nthe results with the community.\n\nA live instance can be found at [https://higlass.io](https://higlass.io). A [Docker container](https://github.com/higlass/higlass-docker) is available for running an instance locally, although we recommend using the [higlass-manage](https://github.com/pkerpedjiev/higlass-manage) package to start, stop and configure local instances.\n\nFor documentation about how to use and install HiGlass, please visit [https://docs.higlass.io](https://docs.higlass.io).\n\n### Citation\n\nKerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., ... & Gehlenborg, N. *HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps.* Genome Biology (2018): 19:125. https://doi.org/10.1186/s13059-018-1486-1\n\n### Example\n\n

\n \n

\n\n### Development\n\nTo run higlass from its source code simply run the following:\n\n```\nnpm clean-install // use --legacy-peer-deps if you get peer dependency errors\nnpm run start\n```\n\nThis starts a server in development mode at http://localhost:5173/.\n\n> **Warning** \n> The following examples need to be migrated to the latest build.\n> Once started, a list of the examples can be found at [http://localhost:8080/examples.html](http://localhost:8080/examples.html).\n> Template viewconfs located at `/docs/examples/viewconfs` can viewed directly at urls such as [http://localhost:8080/apis/svg.html?/viewconfs/overlay-tracks.json](http://localhost:8080/apis/svg.html?/viewconfs/overlay-tracks.json).\n\n\n### Tests\n\nThe tests for the React components and API functions are located in the `test` directory.\nTests are run with [`vitest`](https://vitest.dev/).\n\nUseful commands:\n\n- Run all tests in the browser: `npm test`\n\n**Troubleshooting:**\n\n- If the installation fails due to `sharp` > `node-gyp` try installing the node packages using `python2`:\n\n ```\n npm ci --python=/usr/bin/python2 && rm -rf node_modules/node-sass && npm ci\n ```\n\n### API\n\nHiGlass provides an API for controlling the component from with JavaScript. Below is a [minimal working example](docs/examples/others/minimal-working-example.html) to get started and the complete documentation is availabe at [docs.higlass.io](http://docs.higlass.io/javascript_api.html).\n\n```html\n\n\n \n Minimal Working Example · HiGlass\n \n \n\n \n\n \n \n \n \n \n\n\n\n\n```\n\n### Related\n\n[![diagram of related tools](https://docs.google.com/drawings/d/e/2PACX-1vSCiCzfQ8FEyHPFSq7jJD6XmzC760xH1Zr4FIcCMzFmqAlrmYEBMId8gM42uz0okmvuEaxetyPPZ9VG/pub?w=600&h=450)](https://docs.google.com/drawings/d/1Xedi5ZRtbRdt2g20qpl_lWs4BMqc2DKZ2ZOoJvpHw9U/edit)\n\n* [HiGlass Clodius](https://github.com/higlass/clodius) - Package that provides implementations for aggregation and tile generation for many common 1D and 2D data types\n* [HiGlass Python](https://github.com/higlass/higlass-python) - Python bindings to the HiGlass for tile serving, view config generation, and Jupyter Notebook + Lab integration.\n* [HiGlass Manage](https://github.com/higlass/higlass-manage) - Easy to use interface for deploying a local HiGlass instance\n* [HiGlass Docker](https://github.com/higlass/higlass-docker) - Build an image containing all the components necessary to deploy HiGlass\n* [HiGlass Server](https://github.com/higlass/higlass-server) - Server component for serving multi-resolution data\n* [HiGlass App](https://github.com/higlass/higlass-app) - The code for the web application hosted at https://higlass.io\n* [Cooler](https://github.com/mirnylab/cooler) - Package for efficient storage of and access to sparse 2D data\n\n### License\n\nHiGlass is provided under the MIT License.\n","readmeFilename":"README.md"}