scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
This tool helps biologists and researchers analyze single-cell gene expression data to understand cell types and states. It takes raw gene expression measurements from individual cells and helps visualize, cluster, and identify differences between cell populations. It's used by scientists working with large-scale single-cell omics data.
2,367 stars. Used by 27 other packages. Actively maintained with 20 commits in the last 30 days. Available on PyPI.
Use this if you need to process, analyze, and visualize large datasets of single-cell gene expression to uncover biological insights efficiently.
Not ideal if you are working with bulk RNA sequencing data or need a tool for general-purpose statistical analysis outside of single-cell genomics.
Stars
2,367
Forks
719
Language
Python
License
BSD-3-Clause
Category
Last pushed
Mar 13, 2026
Commits (30d)
20
Dependencies
22
Reverse dependents
27
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