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.

• Discuss development on GitHub.

• Read the documentation.

• Ask questions on the scverse Discourse.

• Install via pip install anndata or conda install anndata -c conda-forge.

• See Scanpy’s documentation for usage related to single cell data. anndata was initially built for Scanpy.

anndata is part of the scverse project (website, governance) and is fiscally sponsored by NumFOCUS. 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.

Latest additions

See Release notes, particularly Version 0.10 for the current release, and the .feature fragments for the upcoming release,

News

Muon paper published 2022-02-02

Muon has been published in Genome Biology [Bredikhin22]. Muon is a framework for multimodal data built on top of AnnData.

Check out Muon and its datastructure MuData.

COVID-19 datasets distributed as h5ad 2020-04-01

In a joint initiative, the Wellcome Sanger Institute, the Human Cell Atlas, and the CZI distribute datasets related to COVID-19 via anndata’s h5ad files: covid19cellatlas.org.