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 0.10

0.10.0rc1 2023-09-09

Note

anndata 0.10.0 is currently available as a release candidate for testing. You can install this version of anndata with:

pip install -U --pre anndata

We expect to make a full release by October.

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 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

Breaking changes

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

• Removal of deprecated dtype argument to AnnData constructor #1126 @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.

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.