Monthly downloads
58.5K
Weekly downloads
14.9K
GitHub stars
1.7K
Downloads in the 30 and 7 days to October 10, 2026. Refreshed weekly.
Package Information
Latest Version
Requires Python
>=3.12
Licence
BSD 3-Clause License
Last Release
1 month ago
Author
The scvi-tools development team
First Release
September 17, 2020
Total Releases
101
Python Versions
3.12
3.13
3.14
No reported malware or high/critical advisories · Details
The current version has no OSV.dev malware reports and no critical or high-severity vulnerabilities.
Package Insights
Score breakdown - each component scores 0-100, weighted by percentage
Maintenance
90
Popularity
72
Adoption
67
Community
80
Provenance
100
How the maintenance status was determined
Last commit
9 days ago
Monthly downloads
58,494
•
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
58,494
Stars
1,704
Stars per 1k downloads
29.13
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
2,134
Month daily avg
1,950
Momentum
+9.5%
((week_daily_avg - month_daily_avg) / month_daily_avg) * 100More insights and metrics
Python version support tiers
requires_python
>=3.12
Cutting Edge
Minimum supported version is 3.14 or newer
•
Modern
Minimum supported version is 3.11 to 3.13
Legacy
Supports 3.10 or older (or Python 2)
Unknown
No requires_python specified or unparseable
License categories
License
BSD 3-Clause License
•
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
36 days ago
Total releases
101
Releases/year
16.6
•
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
93
Monthly downloads
58,494
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
87
Issue Burden
7.6
per 1k stars
Discussions
3.5
per 1k stars
Fork Ratio
19.5%
contrib / forks
Stale Release
No
PR Velocity
Quiet
Not all downloads include detailed metadata. Breakdowns reflect the subset that does.
Downloads by OS
Linux
835
macOS
127
Windows
53
Python Versions
3.11
37.6%
370
3.12
24.0%
236
3.10
21.1%
208
3.13
12.6%
124
3.14
4.8%
47
Top Countries
1.
US
849
US
2.
CN
96
CN
3.
SG
62
SG
4.
DE
61
DE
5.
HK
19
HK
6.
NL
18
NL
7.
GB
16
GB
8.
IE
16
IE
9.
JP
15
JP
10.
IN
12
IN
Weekly Downloads
GitHub Stars
Dependencies
20
- anndata
- docrep >=0.3.2
- joblib
- lightning >=2
- ml-collections
- mudata
- numba >=0.60
- numpy
- pandas
- pyro-ppl
- rich
- scanpy >=1.10
- scikit-learn
- scipy
- sparse >=0.14
- tensorboard
- torch
- torchmetrics
- tqdm
- xarray
176 optional dependencies
-
annbatch>=0.2[tutorials]extra == "tutorials"
-
annbatch>=0.2[all]extra == "all"
-
annbatch>=0.2[dataloaders]extra == "dataloaders"
-
biomart[tutorials]extra == "tutorials"
-
biomart[all]extra == "all"
-
biopython>=1.81[tutorials]extra == "tutorials"
-
biopython>=1.81[all]extra == "all"
-
biopython>=1.81[optional]extra == "optional"
-
biopython>=1.81[regseq]extra == "regseq"
-
boto3[hub]extra == "hub"
-
boto3[all]extra == "all"
-
boto3[optional]extra == "optional"
-
boto3[tutorials]extra == "tutorials"
-
captum[tutorials]extra == "tutorials"
-
captum[all]extra == "all"
-
captum[interpretability]extra == "interpretability"
-
captum[optional]extra == "optional"
-
cell2location[tutorials]extra == "tutorials"
-
cell2location[all]extra == "all"
-
cellxgene-census[tutorials]extra == "tutorials"
-
cellxgene-census[all]extra == "all"
-
cellxgene-census[dataloaders]extra == "dataloaders"
-
cugraph-cu12>=24[rapids-cuda12]extra == "rapids-cuda12"
-
cugraph-cu13>=24[rapids-cuda13]extra == "rapids-cuda13"
-
cuml-cu12>=24[rapids-cuda12]extra == "rapids-cuda12"
-
cuml-cu13>=24[rapids-cuda13]extra == "rapids-cuda13"
-
cupy[rapids]extra == "rapids"
-
cupy-cuda12x[rapids-cuda12]extra == "rapids-cuda12"
-
cupy-cuda12x[cuda]extra == "cuda"
-
cupy-cuda13x[rapids-cuda13]extra == "rapids-cuda13"
-
cupy-cuda13x[cuda13]extra == "cuda13"
-
dask[optional]extra == "optional"
-
dask[parallel]extra == "parallel"
-
dask[tutorials]extra == "tutorials"
-
dask[all]extra == "all"
-
decoupler[tutorials]extra == "tutorials"
-
decoupler[all]extra == "all"
-
decoupler[interpretability]extra == "interpretability"
-
decoupler[optional]extra == "optional"
-
dvc[optional]extra == "optional"
-
dvc[all]extra == "all"
-
dvc[hub]extra == "hub"
-
dvc[tutorials]extra == "tutorials"
-
fastcluster[optional]extra == "optional"
-
fastcluster[all]extra == "all"
-
fastcluster[tutorials]extra == "tutorials"
-
fcswrite[optional]extra == "optional"
-
fcswrite[all]extra == "all"
-
fcswrite[file-sharing]extra == "file-sharing"
-
fcswrite[tutorials]extra == "tutorials"
-
gdown[optional]extra == "optional"
-
gdown[tutorials]extra == "tutorials"
-
gdown[file-sharing]extra == "file-sharing"
-
gdown[all]extra == "all"
-
genomepy[all]extra == "all"
-
genomepy[tutorials]extra == "tutorials"
-
genomepy[regseq]extra == "regseq"
-
genomepy[optional]extra == "optional"
-
geomloss[tutorials]extra == "tutorials"
-
geomloss[optional]extra == "optional"
-
geomloss[diagvi]extra == "diagvi"
-
geomloss[all]extra == "all"
-
gputil[tutorials]extra == "tutorials"
-
gputil[optional]extra == "optional"
-
gputil[mlflow]extra == "mlflow"
-
gputil[all]extra == "all"
-
huggingface-hub[tutorials]extra == "tutorials"
-
huggingface-hub[optional]extra == "optional"
-
huggingface-hub[hub]extra == "hub"
-
huggingface-hub[all]extra == "all"
-
hyperopt>=0.2[optional]extra == "optional"
-
hyperopt>=0.2[all]extra == "all"
-
hyperopt>=0.2[autotune]extra == "autotune"
-
hyperopt>=0.2[tutorials]extra == "tutorials"
-
igraph[tutorials]extra == "tutorials"
-
igraph[all]extra == "all"
-
igraph[optional]extra == "optional"
-
jupyter[tutorials]extra == "tutorials"
-
jupyter[all]extra == "all"
-
lamindb>=1.12.1[all]extra == "all"
-
lamindb>=1.12.1[dataloaders]extra == "dataloaders"
-
lamindb>=1.12.1[tutorials]extra == "tutorials"
-
leidenalg[all]extra == "all"
-
leidenalg[tutorials]extra == "tutorials"
-
leidenalg[optional]extra == "optional"
-
matplotlib[all]extra == "all"
-
matplotlib[tutorials]extra == "tutorials"
-
mlflow>=3.9[optional]extra == "optional"
-
mlflow>=3.9[mlflow]extra == "mlflow"
-
mlflow>=3.9[all]extra == "all"
-
mlflow>=3.9[tutorials]extra == "tutorials"
-
mlx[metal]extra == "metal"
-
mlx-metal[metal]extra == "metal"
-
muon[optional]extra == "optional"
-
muon[all]extra == "all"
-
muon[autotune]extra == "autotune"
-
muon[tutorials]extra == "tutorials"
-
nvidia-ml-py[all]extra == "all"
-
nvidia-ml-py[mlflow]extra == "mlflow"
-
nvidia-ml-py[optional]extra == "optional"
-
nvidia-ml-py[tutorials]extra == "tutorials"
-
nvidia-nccl-cu12[cuda]sys_platform == "linux" and extra == "cuda"
-
nvidia-nccl-cu13[cuda13]sys_platform == "linux" and extra == "cuda13"
-
plotnine[all]extra == "all"
-
plotnine[optional]extra == "optional"
-
plotnine[tutorials]extra == "tutorials"
-
pooch[optional]extra == "optional"
-
pooch[tutorials]extra == "tutorials"
-
pooch[file-sharing]extra == "file-sharing"
-
pooch[all]extra == "all"
-
psutil[mlflow]extra == "mlflow"
-
psutil[tutorials]extra == "tutorials"
-
psutil[all]extra == "all"
-
psutil[optional]extra == "optional"
-
pynndescent[optional]extra == "optional"
-
pynndescent[all]extra == "all"
-
pynndescent[tutorials]extra == "tutorials"
-
rapids-singlecell[rapids]extra == "rapids"
-
rapids-singlecell-cu12[rapids-cuda12]extra == "rapids-cuda12"
-
rapids-singlecell-cu13[rapids-cuda13]extra == "rapids-cuda13"
-
ray[all]sys_platform != "win32" and extra == "all"
-
ray[autotune]sys_platform != "win32" and extra == "autotune"
-
ray[optional]sys_platform != "win32" and extra == "optional"
-
ray[tutorials]sys_platform != "win32" and extra == "tutorials"
-
readfcs[all]extra == "all"
-
readfcs[tutorials]extra == "tutorials"
-
readfcs[optional]extra == "optional"
-
readfcs[file-sharing]extra == "file-sharing"
-
requests[tutorials]extra == "tutorials"
-
requests[optional]extra == "optional"
-
requests[hub]extra == "hub"
-
requests[all]extra == "all"
-
scib-metrics[autotune]extra == "autotune"
-
scib-metrics[all]extra == "all"
-
scib-metrics[optional]extra == "optional"
-
scib-metrics[tutorials]extra == "tutorials"
-
scrublet[all]extra == "all"
-
scrublet[tutorials]extra == "tutorials"
-
seaborn[tutorials]extra == "tutorials"
-
seaborn[all]extra == "all"
-
setuptools<82,>=77.0.3[optional]extra == "optional"
-
setuptools<82,>=77.0.3[all]extra == "all"
-
setuptools<82,>=77.0.3[autotune]extra == "autotune"
-
setuptools<82,>=77.0.3[tutorials]extra == "tutorials"
-
shap[interpretability]extra == "interpretability"
-
shap[optional]extra == "optional"
-
shap[tutorials]extra == "tutorials"
-
shap[all]extra == "all"
-
squidpy>=1.6[tutorials]extra == "tutorials"
-
squidpy>=1.6[all]extra == "all"
-
tiledbsoma[dataloaders]extra == "dataloaders"
-
tiledbsoma[all]extra == "all"
-
tiledbsoma[tutorials]extra == "tutorials"
-
tiledbsoma-ml[dataloaders]extra == "dataloaders"
-
tiledbsoma-ml[tutorials]extra == "tutorials"
-
tiledbsoma-ml[all]extra == "all"
-
torch-geometric[tutorials]extra == "tutorials"
-
torch-geometric[all]extra == "all"
-
torch-geometric[diagvi]extra == "diagvi"
-
torch-geometric[optional]extra == "optional"
-
torch-xla[tpu]extra == "tpu"
-
torchaudio[metal]extra == "metal"
-
torchaudio[cuda13]extra == "cuda13"
-
torchaudio[cuda]extra == "cuda"
-
torchdata[dataloaders]extra == "dataloaders"
-
torchdata[all]extra == "all"
-
torchdata[tutorials]extra == "tutorials"
-
torchvision[cuda13]extra == "cuda13"
-
torchvision[metal]extra == "metal"
-
torchvision[cuda]extra == "cuda"
-
umap-learn>=0.5[tutorials]extra == "tutorials"
-
umap-learn>=0.5[all]extra == "all"
-
zarr[all]extra == "all"
-
zarr[optional]extra == "optional"
-
zarr[parallel]extra == "parallel"
-
zarr[tutorials]extra == "tutorials"
Used By
71
- sciv 5.0K/mo
- exprmat 4.3K/mo
- cell2location 2.5K/mo
- scgpt 2.0K/mo
- popv 1.7K/mo
- tcri 1.6K/mo
- sccairns 977/mo
- drvi-py 874/mo
- pyrovelocity 846/mo
- cpa-tools 841/mo
Repository details
Data and sources
Tracking Since
September 26, 2026
Data Updated
October 11, 2026
Data Freshness
Fresh