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@scverse

scverse

Foundational tools for omics data in the life sciences
README.md

Welcome to scverse®!

scverse

scverse® is a community that develops and maintains foundational tools for single-cell omics data analysis in primarily Python.

Here's how to get started:

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  1. scanpy scanpy Public

    Single-cell analysis in Python. Scales to >100M cells.

    Python 2.6k 780

  2. anndata anndata Public

    Annotated data.

    Python 773 209

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 476

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 599 122

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 398 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 346 67

Repositories

Showing 10 of 97 repositories
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 599 BSD-3-Clause 122 78 (1 issue needs help) 29 Updated Sep 25, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 8 BSD-3-Clause 0 39 3 Updated Sep 25, 2026
  • scverse-misc Public

    Miscellaneous utility code used by scverse packages

    scverse/scverse-misc's past year of commit activity
    Python 5 BSD-3-Clause 2 7 3 Updated Sep 25, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler's past year of commit activity
    Python 295 BSD-3-Clause 38 3 3 Updated Sep 25, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 398 MIT 52 12 12 Updated Sep 25, 2026
  • scanpy Public

    Single-cell analysis in Python. Scales to >100M cells.

    scverse/scanpy's past year of commit activity
    Python 2,569 BSD-3-Clause 780 442 (3 issues need help) 93 Updated Sep 25, 2026
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils's past year of commit activity
    Python 15 MPL-2.0 5 17 (1 issue needs help) 5 Updated Sep 25, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 773 BSD-3-Clause 209 186 (4 issues need help) 84 Updated Sep 25, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 134 BSD-3-Clause 24 8 0 Updated Sep 25, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy's past year of commit activity
    Python 346 MIT 67 9 4 Updated Sep 25, 2026
View all repositories