{"id":17223333,"url":"https://github.com/slowkow/cellguide","last_synced_at":"2025-08-07T23:28:47.433Z","repository":{"id":53267070,"uuid":"268866845","full_name":"slowkow/cellguide","owner":"slowkow","description":"🧭 Navigate single-cell RNA-seq datasets in your web browser.","archived":false,"fork":false,"pushed_at":"2023-07-13T15:02:29.000Z","size":4206,"stargazers_count":28,"open_issues_count":1,"forks_count":4,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-27T14:21:53.364Z","etag":null,"topics":["bioinformatics","cellbrowser","data-visualization","javascript","scrna-seq"],"latest_commit_sha":null,"homepage":"https://cell.guide","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/slowkow.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2020-06-02T17:34:13.000Z","updated_at":"2024-12-11T14:34:55.000Z","dependencies_parsed_at":"2022-08-27T07:01:05.415Z","dependency_job_id":"38a9b586-8f24-47d8-ae4e-336aabafde4c","html_url":"https://github.com/slowkow/cellguide","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/slowkow%2Fcellguide","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/slowkow%2Fcellguide/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/slowkow%2Fcellguide/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/slowkow%2Fcellguide/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/slowkow","download_url":"https://codeload.github.com/slowkow/cellguide/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248800048,"owners_count":21163404,"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":["bioinformatics","cellbrowser","data-visualization","javascript","scrna-seq"],"created_at":"2024-10-15T04:08:04.238Z","updated_at":"2025-04-14T00:22:13.681Z","avatar_url":"https://github.com/slowkow.png","language":"JavaScript","readme":"# Cell Guide 🧭 \n\n[![DOI](https://zenodo.org/badge/268866845.svg)](https://zenodo.org/badge/latestdoi/268866845)\n\nNavigate single-cell RNA-seq datasets in your web browser.\n\nTry it at https://cell.guide\n\n\n### Features\n\n- Display metadata on the UMAP figure\n- Display gene expression on the UMAP figure\n- Aggregate statistics for cell clusters and metadata categories\n- Find any gene, instantly\n- Browse statistics for every gene\n\n\u003ctable\u003e\n  \u003ctr\u003e\n    \u003ctd width=\"20%\"\u003eFlip through metadata variables and see them in low-dimensional space.\u003c/td\u003e\n    \u003ctd\u003e\n      \u003cp align=\"center\"\u003e\n        \u003cimg src=\"https://i.imgur.com/tcYRggc.gif\" width=\"80%\" align=\"center\" /\u003e\n      \u003c/p\u003e\n    \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003ctable\u003e\n  \u003ctr\u003e\n  \u003ctd\u003e\n    \u003cp align=\"center\"\u003e\n      \u003cimg src=\"https://i.imgur.com/zBVTCy9.png\" width=\"80%\" align=\"center\" /\u003e\n    \u003c/p\u003e\n  \u003c/td\u003e\n  \u003ctd width=\"20%\"\u003eSee which donors have similar proportions of different cell clusters.\u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003ctable\u003e\n  \u003ctr\u003e\n  \u003ctd width=\"20%\"\u003eFind any gene and see expression across clusters, faceted by metadata variables.\u003c/td\u003e\n  \u003ctd\u003e\n    \u003cp align=\"center\"\u003e\n      \u003cimg src=\"https://i.imgur.com/KgMw3zN.gif\" width=\"80%\" align=\"center\" /\u003e\n    \u003c/p\u003e\n  \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\nDemo scRNA-seq data from the research article by [Smillie et al. 2019][3].\n\n[3]: https://doi.org/10.1016/j.cell.2019.06.029\n\n\n## Quick Start\n\n### Step 1. Install Cell Browser\n\nWe can install the Cell Browser Python package with pip (we need a specific version):\n\n```\npip install cellbrowser==0.7.15\n```\n\nOr see the [Cell Browser installation instructions](https://cellbrowser.readthedocs.io/installation.html).\n\n### Step 2. Create a browser for your data\n\nSee the [documentation][1] for how to create a Cell Browser for your data.\n\nWhen your browser is working, it should look something like this:\n\n\u003cp align=\"center\"\u003e\n\u003cimg src=\"https://i.imgur.com/N1B2Q5U.png\" width=\"80%\" align=\"center\" /\u003e\n\u003c/p\u003e\n\n### Step 3. Copy Cell Guide files\n\n```bash\n# Get the Cell Guide code\ncurl -s https://codeload.github.com/slowkow/cellguide/tar.gz/master | tar xvz\n \n# Overwrite the Cell Browser files: index.html js/ css/ ext/ img/\ncommand cp -rf cellguide-master/www/* public_html/\n```\n\nFor a complete example, see the [demo.sh](demo.sh) script.\n\nMake sure to refresh your web browser with \u003ckbd\u003e⌘\u003c/kbd\u003e+\u003ckbd\u003eShift\u003c/kbd\u003e+\u003ckbd\u003eR\u003c/kbd\u003e (or \u003ckbd\u003eCtrl\u003c/kbd\u003e+\u003ckbd\u003eShift\u003c/kbd\u003e+\u003ckbd\u003eR\u003c/kbd\u003e on Windows).\n\n[1]: https://cellbrowser.readthedocs.io/basic_usage.html\n\n\n## Dependencies\n\nThe current version of Cell Guide depends on [Cell Browser] by [Maximilian\nHaeussler].\n\n[Cell Browser]: https://github.com/maximilianh/cellBrowser\n[Maximilian Haeussler]: https://github.com/maximilianh\n\nBuilt with:\n\n- [Bootstrap](https://getbootstrap.com)\n- [CSS loaders](https://projects.lukehaas.me/css-loaders/)\n- [d3-legend](https://github.com/susielu/d3-legend)\n- [D3.js](https://d3js.org)\n- [FastBitSet](https://github.com/lemire/FastBitSet.js/)\n- [hcluster.js](https://github.com/cmpolis/hcluster.js/)\n- [jQuery](https://jquery.com)\n- [JSURL2](https://www.npmjs.com/package/@yaska-eu/jsurl2)\n- [pako](https://github.com/nodeca/pako)\n- [palette.js](https://github.com/google/palette.js/tree/master)\n- [papaparse](https://www.papaparse.com/)\n- [tablesort](https://github.com/tristen/tablesort)\n\n\nLet me know what you think! [@slowkow](https://twitter.com/slowkow)\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fslowkow%2Fcellguide","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fslowkow%2Fcellguide","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fslowkow%2Fcellguide/lists"}