scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
Provides integrated preprocessing, clustering, trajectory inference, and differential expression testing via the AnnData data structure for efficient in-memory analysis. Leverages optional Dask integration for out-of-core computation on datasets exceeding available RAM. Part of the broader scverse ecosystem, enabling interoperability with complementary single-cell analysis tools.
2,367 stars and 740,313 monthly downloads. Used by 27 other packages. Actively maintained with 13 commits in the last 30 days. Available on PyPI.
Stars
2,367
Forks
719
Language
Python
License
BSD-3-Clause
Category
Last pushed
Mar 13, 2026
Monthly downloads
740,313
Commits (30d)
13
Dependencies
22
Reverse dependents
27
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