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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:

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  1. scanpy scanpy Public

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

    Python 2.3k 697

  2. anndata anndata Public

    Annotated data.

    Python 702 180

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.5k 435

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 547 103

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 339 79

  6. scirpy scirpy Public

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

    Python 244 41

Repositories

Showing 10 of 71 repositories
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,328 BSD-3-Clause 697 489 (5 issues need help) 74 Updated Jan 19, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 32 BSD-3-Clause 66 7 12 Updated Jan 19, 2026
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 290 MIT 40 18 8 Updated Jan 19, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 3 9 17 1 Updated Jan 19, 2026
  • prelude-runner Public

    Jupyter notebook runner that executes preludes before each cell

    scverse/prelude-runner’s past year of commit activity
    Python 1 Apache-2.0 0 1 0 Updated Jan 19, 2026
  • anndata-plot Public
    scverse/anndata-plot’s past year of commit activity
    Python 8 MIT 3 1 4 Updated Jan 19, 2026
  • session-info2 Public
    scverse/session-info2’s past year of commit activity
    Python 7 MPL-2.0 1 1 0 Updated Jan 19, 2026
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials’s past year of commit activity
    Python 19 BSD-3-Clause 15 12 5 Updated Jan 19, 2026
  • scanpy-tutorials Public

    Scanpy Tutorials.

    scverse/scanpy-tutorials’s past year of commit activity
    Jupyter Notebook 232 BSD-3-Clause 120 15 (1 issue needs help) 1 Updated Jan 19, 2026
  • simple-scvi Public

    Simple scVI implementation

    scverse/simple-scvi’s past year of commit activity
    Python 12 BSD-3-Clause 4 0 3 Updated Jan 19, 2026
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