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.

Citation

If you use anndata in your work, please cite the anndata pre-print as follows:

anndata: Annotated data

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

bioRxiv 2021 Dec 19. doi: 10.1101/2021.12.16.473007.

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

Version 0.11

0.11.0 the future

Features

Bugfix

Documentation

Performance

Breaking

• Removed deprecated modules anndata.core and anndata.readwrite #1197 @ivirshup

Version 0.10

0.10.4 the future

Bugfix

• Only try to use Categorical.map(na_action=…) in actually supported Pandas ≥2.1 #1226 @flying-sheep

• AnnData.__sizeof__() support for backed datasets #1230 @Neah-Ko

• adata[:, []] now returns an AnnData object empty on the appropriate dimensions instead of erroring #1243 @ilan-gold

Documentation

Performance

0.10.3 2023-10-31

Bugfix

• Prevent pandas from causing infinite recursion when setting a slice of a categorical column #1211 @flying-sheep

Documentation

• Stop showing “Support for Awkward Arrays is currently experimental” warnings when reading, concatenating, slicing, or transposing AnnData objects #1182 @flying-sheep

Other updates

• Fail canary CI job when tests raise unexpected warnings. #1182 @flying-sheep

0.10.2 2023-10-11

Bugfix

• Added compatibility layer for packages relying on anndata._core.sparse_dataset.SparseDataset. Note that this API is deprecated and new code should use CSRDataset, CSCDataset, and sparse_dataset() instead. #1185 @ivirshup

• Handle deprecation warning from pd.Categorical.map thrown during anndata.concat #1189 @flying-sheep @ivirshup

• Fixed extra steps being included in IO tracebacks #1193 @flying-sheep

• as_dense argument of write_h5ad no longer writes an array without encoding metadata #1193 @flying-sheep

Performance

• Improved performance of concat_on_disk with dense arrays in some cases #1169 @selmanozleyen

0.10.1 2023-10-08

Bugfix

• Fix ad.concat erroring when concatenating a categorical and object column #1171 @ivirshup

0.10.0 2023-10-06

Features

GPU Support

• Dense and sparse CuPy arrays are now supported #1066 @ivirshup

  • Once you have CuPy arrays in your anndata, use it with: rapids-singlecell from v0.9+

• anndata now has GPU enabled CI. Made possibly by a grant from CZI’s EOSS program and managed via Cirun #1066 #1084 @Zethson @ivirshup

Out of core

• Concatenate on-disk anndata objects with anndata.experimental.concat_on_disk() #955 @selmanozleyen

• AnnData can now hold dask arrays with scipy.sparse.spmatrix chunks #1114 @ivirshup

• Public API for interacting with on disk sparse arrays: sparse_dataset(), CSRDataset, and CSCDataset #765 @ilan-gold @ivirshup

• Improved performance for simple slices of OOC sparse arrays #1131 @ivirshup

Improved errors and warnings

• Improved error messages when combining dataframes with duplicated column names #1029 @ivirshup

• Improved warnings when modifying views of AlingedMappings #1016 @flying-sheep @ivirshup

• AnnDataReadErrors have been removed. The original error is now thrown with additional information in a note #1055 @ivirshup

Documentation

• Added zarr examples to file format docs #1162 @ivirshup

Breaking changes

• anndata.AnnData.transpose() no longer copies unnecessarily. If you rely on the copying behavior, call .copy on the resulting object. #1114 @ivirshup

Other updates

• Bump minimum python version to 3.9 #1117 @flying-sheep

Deprecations

• Deprecate anndata.read, which was just an alias for anndata.read_h5ad() #1108 @ivirshup.

• dtype argument to AnnData constructor is now deprecated #1153 @ivirshup

Bug fixes

• Fix shape inference on initialization when X=None is specified #1121 @flying-sheep

See Release notes for more.

News

Muon paper published 2022-02-02

Muon has been published in Genome Biology [^cite_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.