{"id":38059024,"url":"https://github.com/fabilab/cell_atlas_approximations_compression","last_synced_at":"2026-01-16T20:28:02.236Z","repository":{"id":167093026,"uuid":"626672503","full_name":"fabilab/cell_atlas_approximations_compression","owner":"fabilab","description":"Compression for cell atlas approximations","archived":false,"fork":false,"pushed_at":"2025-02-17T12:56:45.000Z","size":366,"stargazers_count":0,"open_issues_count":6,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-17T13:39:26.837Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/fabilab.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-04-12T00:04:29.000Z","updated_at":"2025-02-17T12:56:49.000Z","dependencies_parsed_at":null,"dependency_job_id":"f1f2f06e-6563-4a12-bcff-a82b7809165c","html_url":"https://github.com/fabilab/cell_atlas_approximations_compression","commit_stats":null,"previous_names":["fabilab/cell_atlas_approximations_compression"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/fabilab/cell_atlas_approximations_compression","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabilab%2Fcell_atlas_approximations_compression","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabilab%2Fcell_atlas_approximations_compression/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabilab%2Fcell_atlas_approximations_compression/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabilab%2Fcell_atlas_approximations_compression/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fabilab","download_url":"https://codeload.github.com/fabilab/cell_atlas_approximations_compression/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabilab%2Fcell_atlas_approximations_compression/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28482267,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2026-01-16T20:28:02.109Z","updated_at":"2026-01-16T20:28:02.222Z","avatar_url":"https://github.com/fabilab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"https://raw.githubusercontent.com/fabilab/cell_atlas_approximations/main/figures/figure_Approximation.png\" width=\"150\"\u003e\n\n# Cell Atlas Approximations - Compression\nCell atlases such as Tabula Muris and Tabula Sapiens are multi-organ single cell omics data sets describing entire organisms. A cell atlas approximation is a lossy and lightweight compression of a cell atlas that can be streamed via the internet.\n\nThis project enables biologists, doctors, and data scientist to quickly find answers for questions such as:\n\n- *What types of cells populate the human heart?*\n- *What is the expression of a specific gene across cell types in C elegans?*\n- *What are the marker genes of a specific cell type in mouse pancreas*?\n- *What fraction of cells (of a specific type) express a gene of interest?*\n\nTo answer these questions, we construct approximations from all kinds of cell atlases using the code in this repo.\n\n**NOTE:** At this stage, this repo is designed for internal use and made public for transparency. End users are expected to interact with the atlas approximations using the [web interface](https://atlasapprox.org) or the [API](https://atlasapprox.readthedocs.io).\n\n## Available approximations\n\n| Organism | Organs | Publication |\n| --- | --- | --- |\n| homo sapiens | Bone marrow, heart, kidney, colon, pancreas, lung, tongue | https://www.science.org/doi/10.1126/science.abl4896 |\n| mus musculus | Bone marrow, heart, kidney, colon, pancreas, lung, tongue | https://www.nature.com/articles/s41586-020-2496-1 |\n| microcebus myoxinus | Bone marrow, heart, kidney, colon, pancreas, lung, tongue | https://www.biorxiv.org/content/10.1101/2021.12.12.469460v2 |\n| caenorhabditis elegans | whole organism | https://www.science.org/doi/10.1126/science.aam8940 |\n| drosophila melanogaster | Antenna, haltere, heart, intestines, leg, male reproductive glands, malpighian tubule, oenocyte, ovary, proboscis, skin, testis, trachea, wing | https://doi.org/10.1126/science.abk2432 |\n| danio rerio | whole embryo | https://www.science.org/doi/10.1126/science.aar4362 |\n| hofstenia miamia | whole organism | https://www.nature.com/articles/s41467-023-38016-4 |\n| schmidtea mediterraea | whole organism | https://www.science.org/doi/10.1126/science.aaq1736 |\n| schistosoma mansoni | whole organism | https://www.nature.com/articles/s41467-020-20794-w |\n| spongilla lacustris | whole organism | https://www.science.org/doi/10.1126/science.abj2949 |\n| stylophora pistillata | whole organism | https://www.sciencedirect.com/science/article/pii/S0092867421004402 |\n| amphimedon queenslandica | whole organism | https://www.nature.com/articles/s41559-018-0575-6 |\n| mnemiopsis leidy | whole organism | https://www.nature.com/articles/s41559-018-0575-6 |\n| trichoplax adhaerens | whole organism | https://www.nature.com/articles/s41559-018-0575-6 |\n| xenopus laevis | Bladder, bone marrow, brain, eye, heart, intestine, kidney, liver, lung, muscle, ovary, oviduct, pancreas, skin, spleen, stomach, testis | https://www.nature.com/articles/s41467-022-31949-2 |\n\n\n## Proposing a new atlas approximation\nIf you would like to propose an additional cell atlas to be added to the list of approximations, please open an [issue](https://github.com/fabilab/cell_atlas_approximations_compression/issues/new/choose) and specify:\n\n- a hyperlink to a publication where the atlas is described\n- a hyperlink to a data source where the table of counts can be downloaded\n- any information you might have about cell type annotation\n- the reason why you would like to have that atlas added here\n\nThank you for your time.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffabilab%2Fcell_atlas_approximations_compression","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffabilab%2Fcell_atlas_approximations_compression","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffabilab%2Fcell_atlas_approximations_compression/lists"}