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scverse

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

scverse

Welcome to 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:

Pinned Loading

  1. scanpy scanpy Public

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

    Python 2.4k 719

  2. anndata anndata Public

    Annotated data.

    Python 718 184

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 444

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 552 108

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 353 85

  6. scirpy scirpy Public

    A scanpy extension to analyse single-cell TCR and BCR data.

    Python 246 43

Repositories

Showing 10 of 75 repositories
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 74 BSD-3-Clause 18 78 8 Updated Mar 11, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 552 BSD-3-Clause 108 63 (1 issue needs help) 25 Updated Mar 11, 2026
  • annbatch Public

    Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

    scverse/annbatch’s past year of commit activity
    Python 26 MIT 3 21 10 Updated Mar 11, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 158 16 30 5 Updated Mar 11, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler’s past year of commit activity
    Python 261 BSD-3-Clause 34 5 1 Updated Mar 11, 2026
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 313 MIT 42 14 8 Updated Mar 10, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,365 BSD-3-Clause 719 489 (5 issues need help) 79 Updated Mar 10, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 353 BSD-3-Clause 85 255 12 Updated Mar 10, 2026
  • anndata-plot Public
    scverse/anndata-plot’s past year of commit activity
    Python 8 MIT 3 1 4 Updated Mar 10, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy’s past year of commit activity
    Python 291 MIT 52 31 5 Updated Mar 10, 2026
View all repositories