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.
Ask questions on the scverse Discourse.
pip install anndataor
conda install anndata -c conda-forge.
Consider citing the anndata paper.
See Scanpy’s documentation for usage related to single cell data. anndata was initially built for Scanpy.
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
COVID-19 datasets distributed as
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.
0.9.0 the future
Bump minimum python version to 3.8 PR 820 ivirshup
0.8.1 the future
Fix warning from
rename_categoriesPR 790 I Virshup
Remove backwards compat checks for categories in
unswhen we can tell the file is new enough PR 790 I Virshup
0.8.0 14th March, 2022
The on disk format of AnnData objects has been updated with this release.
Previous releases of
anndata will not be able to read all files written by this version.
For discussion of possible future solutions to this issue, see issue 698
Internal handling of IO has been overhauled.
This should make it much easier to support new datatypes, use partial access, and use
AnnData internally in other formats.
Each element should be tagged with an
encoding_version. See updated docs on the file format
Support for nullable integer and boolean data arrays. More data types to come!
h5adfiles written from Julia PR 569 I Kats
Many logging messages that should have been warnings are now warnings PR 650 I Virshup
Fixed deepcopy of a copy of a view retaining sparse matrix view mixin type PR 670 M Klein
xlrddependency I Virshup
vardataframes are no longer copied by default on
AnnDatainstantiation issue 371 I Virshup
Fixed issue where
.copywas creating sparse matrices views when copying PR 670 michalk8
Fixed issue where
.Xmatrix read in from
zarrwould always have
float32values PR 701 I Virshup
obspin the output PR 404 G Eraslan
xlrddropped as a hard dependency