No known security advisories.
The current version has no OSV.dev malware reports and no critical or high-severity vulnerabilities.
anndata has 1.8M monthly downloads and 756 GitHub stars. Version 0.12.19 supports Python 3.11+, first published in 2017.
It is actively maintained under a permissive license, last released in Jul 2026.
It is built on top of array-api-compat, h5py and legacy-api-wrap. It is used by 957 tracked packages, including scanpy, mudata and pydeseq2.
GitHub topics include scanpy, data-science and transcriptomics.
Package Insights
Score breakdown - each component scores 0-100, weighted by percentage
Maintenance
100
Popularity
63
Adoption
70
Community
80
Provenance
100
How the maintenance status was determined
Last commit
3 days ago
Monthly downloads
1,833,012
•
Active
Activity within 30 days
Stable
Activity within 31-180 days
Minimal
Activity within 181-365 days, or no activity data
At Risk
No activity for > 365 days, but > 10,000 monthly downloads
Archived
Repository flagged as archived on GitHub
How the popularity category was determined
Monthly downloads
1,833,012
Stars
756
Stars per 1k downloads
0.41
Industry Standard
> 10,000,000 monthly downloads
•
Hidden Gem
< 0.5 stars per 1k downloads and > 100,000 monthly downloads
Community Favorite
> 5 stars per 1k downloads
Rising Star
Balanced ratio of stars to downloads
Unknown
Fewer than 1,000 monthly downloads, or no star data
How download momentum is calculated
Week daily avg
55,482
Month daily avg
61,100
Momentum
-9.2%
((week_daily_avg - month_daily_avg) / month_daily_avg) * 100Python version support tiers
requires_python
>=3.11
Cutting Edge
Minimum supported version is 3.12 or newer
•
Modern
Minimum supported version is 3.9, 3.10, or 3.11
Legacy
Supports 3.8 or older (or Python 2)
Unknown
No requires_python specified or unparseable
License categories
License
BSD-3-Clause
•
Permissive
MIT, Apache, BSD, ISC, Unlicense, CC0, etc.
Copyleft
GPL, LGPL, AGPL, MPL, EPL, etc.
Proprietary
Commercial, all rights reserved, custom EULAs
Unknown
No license specified, or none of the above match
How the release cadence was determined
Last release
4 days ago
Total releases
120
Releases/year
13.8
•
Rapid
Last release within 365 days and > 12 releases/year
Regular
Last release within 365 days
Slow
Last release 366-730 days ago
Stalled
Last release > 730 days ago, or no releases
Unknown
No usable release date available
How contributor risk was determined
Contributors
56
Monthly downloads
1,833,012
High Load
≤ 2 contributors and ≥ 50,000 monthly downloads
Moderate Load
< 10 contributors and ≥ 500,000 monthly downloads
Low Load
< 25 contributors and ≥ 5,000,000 monthly downloads, or sole maintainer with ≥ 10,000 monthly downloads
•
Balanced
Enough contributors for the package's popularity
Unknown
No contributor data available
Engagement
75
Issue Burden
251.3
per 1k stars
Discussions
0.0
per 1k stars
Fork Ratio
28.0%
contrib / forks
Stale Release
No
PR Velocity
Active
Weekly Downloads
GitHub Stars
Not all downloads include detailed metadata. Breakdowns reflect the subset that does.
Downloads by OS
Linux
27.4K
macOS
1.8K
Windows
1.1K
Python Versions
3.12
51.8%
15.2K
3.11
21.8%
6.4K
3.10
11.4%
3.3K
3.13
10.6%
3.1K
3.14
4.3%
1.3K
Top Countries
1.
US
23.4K
US
2.
SG
1.9K
SG
3.
ID
1.6K
ID
4.
CN
1.1K
CN
5.
IE
998
IE
6.
DE
323
DE
7.
JP
265
JP
8.
HK
209
HK
9.
GB
163
GB
10.
NL
131
NL
Dependencies
10
- array-api-compat >=1.7.1
- h5py >=3.8
- legacy-api-wrap
- natsort
- numpy >=1.26
- packaging >=24.2
- pandas !=2.1.2,<3,>=2.1.0
- scipy !=1.17.0,>=1.12
- scverse-misc >=0.0.3
- zarr !=3.0.*,>=2.18.7
64 optional dependencies
- aiohttp[lazy]
- aiohttp[test]
- awkward[test]
- awkward[test-min]
- awkward[doc]
- boltons[test]
- boltons[test-min]
- cupy[gpu]
- cupy-cuda11x[cu11]
- cupy-cuda12x[cu12]
- dask[test-min]
- dask[dask]
- dask[doc]
- dask[lazy]
- dask[test]
- filelock[test]
- filelock[test-min]
- ipython[doc]
- joblib[test-min]
- joblib[test]
- loompy[test-min]
- loompy[test]
- matplotlib[test-min]
- matplotlib[test]
- myst-nb[doc]
- myst-parser[doc]
- openpyxl[test-min]
- openpyxl[test]
- pooch[test]
- pooch[test-min]
- pyarrow[test]
- pyarrow[test-min]
- pytest[test-min]
- pytest[test]
- pytest-cov[test]
- pytest-cov[test-min]
- pytest-memray[test]
- pytest-memray[test-min]
- pytest-mock[test]
- pytest-mock[test-min]
- pytest-randomly[test-min]
- pytest-randomly[test]
- pytest-xdist[test-min]
- pytest-xdist[test]
- requests[test]
- requests[lazy]
- scanpy[test-min]
- scanpy[test]
- scanpydoc[doc]
- scikit-learn[test]
- scikit-learn[test-min]
- scverse-misc[doc]
- sphinx[doc]
- sphinx-autodoc-typehints[doc]
- sphinx-book-theme[doc]
- sphinx-copybutton[doc]
- sphinx-design[doc]
- sphinx-issues[doc]
- sphinxext-opengraph[doc]
- towncrier[dev-doc]
- towncrier[doc]
- towncrier[dev]
- xarray[test]
- xarray[lazy]
Used By
957
- scanpy
- mudata
- pydeseq2
- spatialdata
- anndata2ri
- tiledbsoma
- scvi-tools
- somacore
- cellxgene-census
- alphagenome
- crested
- annsel
- squidpy
- decoupler
- tcrsift
- muon
- readfcs
- grelu
- illico
- spatialdata-io
- scib-metrics
- liana
- sciv
- scvelo
- napari-spatialdata
- pdex
- linkapy
- scib
- doubletdetection
- scimap
- cellrank
- cell-eval
- tiledb-cloud
- omicverse
- palantir
- snapatac2
- crispr-ambiguous-mapping
- ngio
- scirpy
- scte-quant
- anndataoom
- infercnvpy
- lingergrn
- m3drop
- single-cell-metabolomics
- annbatch
- aiagents4pharma
- exprmat
- celldega
- adpbulk
GitHub Topics
Tags from the package's GitHub repository describing what it does.
Package Information
License
BSD-3-Clause
First Release
November 7, 2017
Last Release
5 days ago
Last Commit
4 days ago
Latest Version
0.12.19
Total Releases
120
Contributors
56
Open PRs
73
Archived
No
Author
Philipp Angerer, Alex Wolf, Isaac Virshup, Sergei Rybakov, Ilan Gold
Python Versions
3
3.11
3.12
3.13
3.14
Wheels
py3
Tracking Since
January 6, 2026
Data Updated
July 5, 2026
Data Freshness
Fresh