{"id":13735872,"url":"https://github.com/higlass/higlass","last_synced_at":"2025-05-15T02:04:36.931Z","repository":{"id":39006607,"uuid":"56026057","full_name":"higlass/higlass","owner":"higlass","description":"Fast, flexible and extensible genome browser.","archived":false,"fork":false,"pushed_at":"2025-03-18T00:37:28.000Z","size":161462,"stargazers_count":320,"open_issues_count":31,"forks_count":52,"subscribers_count":20,"default_branch":"develop","last_synced_at":"2025-04-03T03:39:21.550Z","etag":null,"topics":["gehlenborglab","genomics","hi-c","higlass","visualization"],"latest_commit_sha":null,"homepage":"http://higlass.io","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/higlass.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.bib","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-04-12T02:58:30.000Z","updated_at":"2025-03-26T17:05:57.000Z","dependencies_parsed_at":"2023-10-17T00:04:26.212Z","dependency_job_id":"af6a0120-a72f-4219-80a3-ed49ab512b82","html_url":"https://github.com/higlass/higlass","commit_stats":null,"previous_names":[],"tags_count":287,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/higlass","download_url":"https://codeload.github.com/higlass/higlass/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248166857,"owners_count":21058481,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["gehlenborglab","genomics","hi-c","higlass","visualization"],"created_at":"2024-08-03T03:01:12.393Z","updated_at":"2025-04-10T06:16:56.978Z","avatar_url":"https://github.com/higlass.png","language":"JavaScript","funding_links":[],"categories":["JavaScript"],"sub_categories":[],"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. It\nfeatures synchronized navigation of multiple views as well as continuous\nzooming and panning for navigation across genomic loci and resolutions. It\nsupports visual comparison of genomic (e.g., Hi-C, ChIP-seq, or bed\nannotations) and other data (e.g., geographic maps, gigapixel images, or\nabstract 1D and 2D sequential data) from different experimental conditions and\ncan be used to efficiently identify salient outcomes of experimental\nperturbations, generate new hypotheses, and share the results with the\ncommunity.\n\nA live instance can be found at [https://higlass.io](https://higlass.io). A\n[Docker container](https://github.com/higlass/higlass-docker) is available for\nrunning an instance locally, although we recommend using the\n[higlass-manage](https://github.com/pkerpedjiev/higlass-manage) package to\nstart, stop and configure local instances.\n\nFor documentation about how to use and install HiGlass, please visit\n[https://docs.higlass.io](https://docs.higlass.io).\n\n### Citation\n\nKerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt,\nH., ... \u0026 Gehlenborg, N. *HiGlass: Web-based Visual Exploration and Analysis of\nGenome Interaction Maps.* Genome Biology (2018): 19:125.\nhttps://doi.org/10.1186/s13059-018-1486-1\n\n### Example\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://cloud.githubusercontent.com/assets/2143629/24535936/37ee60ee-15a5-11e7-89aa-434d93cda91d.gif\" /\u003e\n\u003c/p\u003e\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 start\n```\n\nThis starts a server in development mode at http://localhost:5173/.\n\n\u003e **Warning** \n\u003e The following examples need to be migrated to the latest build.\n\u003e Once started, a list of the examples can be found at [http://localhost:8080/examples.html](http://localhost:8080/examples.html).\n\u003e 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### Tests\n\nThe tests for the React components and API functions are located in the `test`\ndirectory. Tests are run with [`vitest`](https://vitest.dev/).\n\nUseful commands:\n\n- Run all tests in the browser: `npm test -- --browser.headless=false`\n\nSee the [contributing guide](./CONTRIBUTING.md) to learn more.\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\u003c!DOCTYPE html\u003e\n  \u003chead\u003e\n    \u003cmeta charset=\"utf-8\"\u003e\n    \u003ctitle\u003eMinimal Working Example \u0026middot; HiGlass\u003c/title\u003e\n    \u003cstyle type=\"text/css\"\u003e\n      html, body {\n        width: 100vw;\n        height: 100vh;\n        overflow: hidden;\n      }\n    \u003c/style\u003e\n  \u003c/head\u003e\n  \u003cbody\u003e\u003c/body\u003e\n  \u003cscript type=\"module\"\u003e\n    import * as hglib from \"https://esm.sh/higlass@1.13\";\n\n    const api = hglib.viewer(\n      document.body,\n      'https://higlass.io/api/v1/viewconfs/?d=default',\n      { bounded: true },\n    );\n  \u003c/script\u003e\n\u003c/html\u003e\n```\n\n### Related\n\n[![diagram of related tools](https://docs.google.com/drawings/d/e/2PACX-1vSCiCzfQ8FEyHPFSq7jJD6XmzC760xH1Zr4FIcCMzFmqAlrmYEBMId8gM42uz0okmvuEaxetyPPZ9VG/pub?w=600\u0026h=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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhiglass%2Fhiglass","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass/lists"}