No known security advisories.
The current version has no OSV.dev malware reports and no critical or high-severity vulnerabilities.
scanpy has 1.2M monthly downloads and 3K GitHub stars. Version 1.12.2 supports Python 3.12+, first published in 2017.
It is actively maintained under a permissive license, last released in Jun 2026.
It is built on top of anndata, certifi and fast-array-utils. It is used by 910 tracked packages, including tiledbsoma, scvi-tools and squidpy.
GitHub topics include machine-learning, data-science and visualize-data.
Package Insights
Score breakdown - each component scores 0-100, weighted by percentage
Maintenance
100
Popularity
76
Adoption
60
Community
100
Provenance
100
How the maintenance status was determined
Last commit
4 days ago
Monthly downloads
1,182,489
•
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
1,182,489
Stars
2,503
Stars per 1k downloads
2.12
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
35,059
Month daily avg
39,416
Momentum
-11.1%
((week_daily_avg - month_daily_avg) / month_daily_avg) * 100Python version support tiers
requires_python
>=3.12
•
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
7 days ago
Total releases
93
Releases/year
10.4
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
179
Monthly downloads
1,182,489
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
80
Issue Burden
191.0
per 1k stars
Discussions
0.0
per 1k stars
Fork Ratio
23.7%
contrib / forks
Stale Release
No
PR Velocity
Quiet
Weekly Downloads
GitHub Stars
Not all downloads include detailed metadata. Breakdowns reflect the subset that does.
Downloads by OS
Linux
21.5K
macOS
1.3K
Windows
570
Python Versions
3.12
50.4%
11.0K
3.11
19.7%
4.3K
3.8
14.7%
3.2K
3.13
7.6%
1.7K
3.10
7.6%
1.6K
Top Countries
1.
US
15.5K
US
2.
HK
3.2K
HK
3.
ID
1.6K
ID
4.
SG
1.5K
SG
5.
CN
713
CN
6.
IE
243
IE
7.
JP
204
JP
8.
VN
134
VN
9.
DE
133
DE
10.
FI
121
FI
Dependencies
24
- anndata >=0.10.8
- certifi
- fast-array-utils >=1.4
- h5py >=3.11
- joblib
- legacy-api-wrap >=1.5
- matplotlib !=3.11,!=3.11.0rc1,!=3.11.0rc2,>=3.10
- natsort
- networkx >=2.8.8
- numba >=0.60
- numpy >=2
- packaging >=25
- pandas >=2.3
- patsy
- pynndescent >=0.5.13
- scikit-learn >=1.6
- scipy >=1.13
- scverse-misc >=0.0.6
- seaborn >=0.13.2
- session-info2
- statsmodels >=0.14.5
- tqdm
- typing-extensions
- umap-learn >=0.5.12
21 optional dependencies
- anndata[dask]
- anndata[dask-ml]
- bbknn[bbknn]
- colour-science[plotting]
- cudf[rapids]
- cugraph[rapids]
- cuml[rapids]
- dask[dask-ml]
- dask[dask]
- dask-ml[dask-ml]
- harmonypy[harmony]
- igraph[leiden]
- igraph[paga]
- igraph[louvain]
- leidenalg[leiden]
- louvain[louvain]
- magic-impute[magic]
- scanorama[scanorama]
- scikit-image[scrublet]
- scikit-misc[skmisc]
- setuptools[louvain]
Used By
910
- tiledbsoma
- scvi-tools
- squidpy
- spatialdata-plot
- tcrsift
- sure-tools
- muon
- spatialdata-io
- scib-metrics
- celltypist
- liana
- sciv
- scvelo
- napari-spatialdata
- linkapy
- scib
- densityflow
- doubletdetection
- scimap
- cellrank
- cell-eval
- hmap-tool
- omicverse
- pertpy
- palantir
- scirpy
- clustassesspy
- trackcell
- infercnvpy
- lingergrn
- single-cell-metabolomics
- aiagents4pharma
- celldega
- exprmat
- sopa
- rapids-singlecell
- celloracle
- densityflow2
- uce-model
- scgpt
- checkatlas
- cell-load
- densityflowmo
- spatools
- scatrans
- cellphonedb
- celescope
- dmt-learn
- arc-state
- kb-python
GitHub Topics
Tags from the package's GitHub repository describing what it does.
Package Information
License
BSD-3-Clause
First Release
July 24, 2017
Last Release
1 week ago
Last Commit
5 days ago
Latest Version
1.12.2
Total Releases
93
Contributors
179
Open PRs
88
Archived
No
Author
Adam Gayoso, Alex Wolf, Andrés R. Muñoz-Rojas, Davide Cittaro, Fidel Ramirez, Giovanni Palla, Gokcen Eraslan, Ilan Gold, Isaac Virshup, Lukas Heumos, Malte Luecken, Marius Lange, Philipp Angerer, Sergei Rybakov, Tobias Callies, Tom White
Python Versions
3.12
3.13
3.14
Wheels
py3
Tracking Since
January 6, 2026
Data Updated
July 5, 2026
Data Freshness
Fresh