{"id":13584960,"url":"https://github.com/scverse/anndata","last_synced_at":"2026-01-29T14:16:28.681Z","repository":{"id":37590872,"uuid":"100038377","full_name":"scverse/anndata","owner":"scverse","description":"Annotated data.","archived":false,"fork":false,"pushed_at":"2025-06-23T17:35:19.000Z","size":6112,"stargazers_count":632,"open_issues_count":248,"forks_count":166,"subscribers_count":12,"default_branch":"main","last_synced_at":"2025-06-29T10:01:54.400Z","etag":null,"topics":["anndata","bioinformatics","data-science","machine-learning","scanpy","scverse","transcriptomics"],"latest_commit_sha":null,"homepage":"http://anndata.readthedocs.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/scverse.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"docs/contributing.md","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,"zenodo":null}},"created_at":"2017-08-11T14:10:06.000Z","updated_at":"2025-06-26T10:39:25.000Z","dependencies_parsed_at":"2023-11-07T15:27:40.309Z","dependency_job_id":"394f7055-4fe3-45e3-9aa3-124cb5f8adb2","html_url":"https://github.com/scverse/anndata","commit_stats":{"total_commits":1142,"total_committers":48,"mean_commits":"23.791666666666668","dds":0.6523642732049038,"last_synced_commit":"00f39eba8e412639094c87a62ba935f9d94b6622"},"previous_names":["theislab/anndata"],"tags_count":93,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/anndata","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fanndata","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fanndata/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fanndata/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fanndata/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/anndata/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fanndata/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996091,"owners_count":23541402,"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":["anndata","bioinformatics","data-science","machine-learning","scanpy","scverse","transcriptomics"],"created_at":"2024-08-01T15:04:37.716Z","updated_at":"2025-12-11T22:49:25.148Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":["Python","Ranked by starred repositories"],"sub_categories":[],"readme":"[![Tests](https://github.com/scverse/anndata/actions/workflows/test-cpu.yml/badge.svg)](https://github.com/scverse/anndata/actions)\n[![Conda](https://img.shields.io/conda/vn/conda-forge/anndata.svg)](https://anaconda.org/conda-forge/anndata)\n[![Coverage](https://codecov.io/gh/scverse/anndata/branch/main/graph/badge.svg?token=IN1mJN1Wi8)](https://codecov.io/gh/scverse/anndata)\n[![Docs](https://readthedocs.com/projects/icb-anndata/badge/?version=latest)](https://anndata.readthedocs.io)\n[![PyPI](https://img.shields.io/pypi/v/anndata.svg)](https://pypi.org/project/anndata)\n[![Downloads](https://static.pepy.tech/badge/anndata/month)](https://pepy.tech/project/anndata)\n[![Downloads](https://static.pepy.tech/badge/anndata)](https://pepy.tech/project/anndata)\n[![Stars](https://img.shields.io/github/stars/scverse/anndata?style=flat\u0026logo=github\u0026color=yellow)](https://github.com/scverse/anndata/stargazers)\n[![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat\u0026colorA=E1523D\u0026colorB=007D8A)](http://numfocus.org)\n\n\u003cimg\n  src=\"https://raw.githubusercontent.com/scverse/anndata/main/docs/_static/img/anndata_schema.svg\"\n  class=\"dark-light\" align=\"right\" width=\"350\" alt=\"image\"\n/\u003e\n\n# anndata - Annotated data\n\nanndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.\n\n- Discuss development on [GitHub](https://github.com/scverse/anndata).\n- Read the [documentation](https://anndata.readthedocs.io).\n- Ask questions on the [scverse Discourse](https://discourse.scverse.org).\n- Install via `pip install anndata` or `conda install anndata -c conda-forge`.\n- See [Scanpy's documentation](https://scanpy.readthedocs.io/) for usage related to single cell data. anndata was initially built for Scanpy.\n\n[//]: # (numfocus-fiscal-sponsor-attribution)\n\nanndata is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\nIf you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\n\u003cdiv align=\"center\"\u003e\n\u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  \u003e\n\u003c/a\u003e\n\u003c/div\u003e\n\n## Public API\n\nOur public API is documented in the [API section][] of these docs.\nWe cannot guarantee the stability of our internal APIs, whether it's the location of a function, its arguments, or something else.\nIn other words, we do not officially support (or encourage users to do) something like `from anndata._core import AnnData` as `_core` is both not documented and contains a [leading underscore][].\nHowever, we are aware that [many users do use these internal APIs][] and thus encourage them to [open an issue][] or migrate to the public API.\nThat is, if something is missing from our public API as documented, for example a feature you wish to be exported publicly, please open an issue.\n\n[api section]: https://anndata.readthedocs.io/en/stable/api.html\n[leading underscore]: https://peps.python.org/pep-0008/#public-and-internal-interfaces\n[many users do use these internal APIs]: https://github.com/search?q=%22anndata._io%22\u0026type=code\n[open an issue]: https://github.com/scverse/anndata/issues/new/choose\n\n\n## Citation\n\nIf you use `anndata` in your work, please cite the `anndata` publication as follows:\n\n\u003e **anndata: Annotated data**\n\u003e\n\u003e Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, F. Alexander Wolf\n\u003e\n\u003e _JOSS_ 2024 Sep 16. doi: [10.21105/joss.04371](https://doi.org/10.21105/joss.04371).\n\nYou can cite the scverse publication as follows:\n\n\u003e **The scverse project provides a computational ecosystem for single-cell omics data analysis**\n\u003e\n\u003e Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle \u0026 Fabian J. Theis\n\u003e\n\u003e _Nat Biotechnol._ 2023 Apr 10. doi: [10.1038/s41587-023-01733-8](https://doi.org/10.1038/s41587-023-01733-8).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fanndata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fanndata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fanndata/lists"}