anndata 0.12.3


pip install anndata

  Latest version

Released: Oct 16, 2025


Meta
Author: Philipp Angerer, Alex Wolf, Isaac Virshup, Sergei Rybakov
Maintainer: Isaac Virshup, Philipp Angerer, Ilan Gold
Requires Python: >=3.11

Classifiers

Environment
  • Console

Framework
  • Jupyter

Intended Audience
  • Developers
  • Science/Research

Natural Language
  • English

Operating System
  • MacOS :: MacOS X
  • Microsoft :: Windows
  • POSIX :: Linux

Programming Language
  • Python :: 3
  • Python :: 3.11
  • Python :: 3.12
  • Python :: 3.13

Topic
  • Scientific/Engineering :: Bio-Informatics
  • Scientific/Engineering :: Visualization

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anndata - Annotated data

anndata 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.

anndata is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

Public API

Our public API is documented in the API section of these docs. We cannot guarantee the stability of our internal APIs, whether it's the location of a function, its arguments, or something else. In 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. However, 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. That 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.

Citation

If you use anndata in your work, please cite the anndata publication as follows:

anndata: Annotated data

Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, F. Alexander Wolf

JOSS 2024 Sep 16. doi: 10.21105/joss.04371.

You can cite the scverse publication as follows:

The scverse project provides a computational ecosystem for single-cell omics data analysis

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 & Fabian J. Theis

Nat Biotechnol. 2023 Apr 10. doi: 10.1038/s41587-023-01733-8.

0.12.3 Oct 16, 2025
0.12.2 Aug 11, 2025
0.12.1 Jul 23, 2025
0.12.0 Jul 16, 2025
0.12.0rc4 Jun 18, 2025
0.12.0rc3 May 20, 2025
0.12.0rc2 May 15, 2025
0.12.0rc1 Apr 09, 2025
0.11.4 Mar 26, 2025
0.11.3 Jan 10, 2025
0.11.2 Jan 07, 2025
0.11.1 Nov 12, 2024
0.11.0 Nov 07, 2024
0.11.0rc3 Oct 14, 2024
0.11.0rc2 Sep 24, 2024
0.11.0rc1 Sep 04, 2024
0.10.9 Aug 28, 2024
0.10.8 Jun 20, 2024
0.10.7 Apr 09, 2024
0.10.6 Mar 11, 2024
0.10.5.post1 Jan 26, 2024
0.10.5 Jan 26, 2024
0.10.4 Jan 04, 2024
0.10.3 Oct 31, 2023
0.10.2 Oct 11, 2023
0.10.1 Oct 08, 2023
0.10.0 Oct 06, 2023
0.10.0rc1 Sep 09, 2023
0.9.2 Jul 25, 2023
0.9.1 Apr 12, 2023
0.9.0 Apr 11, 2023
0.9.0rc1 Feb 21, 2023
0.8.0 Mar 15, 2022
0.8.0rc1 Jan 24, 2022
0.7.8 Nov 09, 2021
0.7.7 Nov 09, 2021
0.7.6 Apr 11, 2021
0.7.5 Nov 12, 2020
0.7.4 Jul 09, 2020
0.7.3 May 20, 2020
0.7.2 May 19, 2020
0.7.2a1 May 18, 2020
0.7.1 Jan 22, 2020
0.7 Jan 22, 2020
0.7rc2 Jan 07, 2020
0.7rc1 Dec 23, 2019
0.6.22.post1 Jul 08, 2019
0.6.22 Jul 06, 2019
0.6.22rc1 Jun 19, 2019
0.6.21 Jun 06, 2019
0.6.20 May 21, 2019
0.6.19 Mar 24, 2019
0.6.18 Jan 29, 2019
0.6.17 Jan 12, 2019
0.6.16 Dec 16, 2018
0.6.15 Dec 12, 2018
0.6.14 Dec 10, 2018
0.6.13 Nov 04, 2018
0.6.12 Oct 29, 2018
0.6.11 Oct 08, 2018
0.6.10 Sep 03, 2018
0.6.9 Aug 20, 2018
0.6.8 Aug 13, 2018
0.6.7 Aug 13, 2018
0.6.6 Jul 23, 2018
0.6.5 Jul 03, 2018
0.6.4 May 25, 2018
0.6.3 May 25, 2018
0.6.2 May 25, 2018
0.6.1 May 15, 2018
0.6 May 01, 2018
0.5.10.post2 Apr 26, 2018
0.5.10.post1 Apr 26, 2018
0.5.10 Apr 17, 2018
0.5.9 Apr 16, 2018
0.5.8.post1 Apr 16, 2018
0.5.8 Mar 29, 2018
0.5.7 Mar 20, 2018
0.5.6 Mar 19, 2018
0.5.5 Mar 05, 2018
0.5.4 Feb 26, 2018
0.5.3 Feb 17, 2018
0.5.2 Feb 15, 2018
0.5.1 Feb 09, 2018
0.5 Feb 09, 2018
0.4.4 Jan 06, 2018
0.4.3 Jan 03, 2018
0.4.2 Dec 29, 2017
0.4.1 Dec 28, 2017
0.4 Dec 24, 2017
0.3.4 Nov 29, 2017
0.3.3 Nov 28, 2017
0.3.2 Nov 28, 2017
0.3.1 Nov 17, 2017
0.3.0.3 Nov 15, 2017
0.3.0.2 Nov 14, 2017
0.3.0.1 Nov 14, 2017
0.3 Nov 14, 2017
0.2.1 Nov 10, 2017
0.2 Nov 10, 2017
0.1 Nov 07, 2017

Wheel compatibility matrix

Platform Python 3
any

Files in release

Extras:
Dependencies:
array-api-compat (>=1.7.1)
h5py (>=3.8)
legacy-api-wrap
natsort
numpy (>=1.26)
packaging (>=24.2)
pandas (!=2.1.2,>=2.1.0)
scipy (>=1.12)
zarr (!=3.0.*,>=2.18.7)