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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 808

  2. anndata anndata Public

    Annotated data.

    Python 784 221

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 481

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 612 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 408 55

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 355 69

Repositories

Showing 10 of 104 repositories
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 5 2 Updated Oct 31, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 408 MIT 55 15 14 Updated Oct 30, 2026
  • pytometry Public

    Flow & mass cytometry analytics.

    scverse/pytometry's past year of commit activity
    Python 61 Apache-2.0 15 12 (2 issues need help) 3 Updated Oct 30, 2026
  • scverse-misc Public

    Miscellaneous utility code used by scverse packages

    scverse/scverse-misc's past year of commit activity
    Python 6 BSD-3-Clause 2 6 2 Updated Oct 30, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 135 BSD-3-Clause 28 9 2 Updated Oct 30, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 784 BSD-3-Clause 221 193 (4 issues need help) 90 Updated Oct 30, 2026
  • zarr-kvikio Public
    scverse/zarr-kvikio's past year of commit activity
    Python 2 MIT 0 0 1 Updated Oct 30, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 404 BSD-3-Clause 106 315 39 Updated Oct 30, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 201 24 50 10 Updated Oct 30, 2026
  • cupy-stubs Public

    Type stubs for CuPy

    scverse/cupy-stubs's past year of commit activity
    Python 4 MPL-2.0 0 1 0 Updated Oct 30, 2026
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