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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 774

  2. anndata anndata Public

    Annotated data.

    Python 769 208

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 472

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 598 120

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 394 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 341 66

Repositories

Showing 10 of 96 repositories
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 392 BSD-3-Clause 93 263 17 Updated Sep 11, 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 11, 2026
  • liana Public

    LIANA+: an all-in-one framework for cell-cell communication

    scverse/liana's past year of commit activity
    Python 315 BSD-3-Clause 37 11 (2 issues need help) 2 Updated Sep 11, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,559 BSD-3-Clause 774 443 (3 issues need help) 91 Updated Sep 11, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,198 BSD-2-Clause 94 25 18 Updated Sep 11, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 598 BSD-3-Clause 120 78 (1 issue needs help) 24 Updated Sep 10, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 769 BSD-3-Clause 208 185 (4 issues need help) 84 Updated Sep 10, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 394 MIT 51 11 9 Updated Sep 10, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,685 BSD-3-Clause 472 12 (1 issue needs help) 11 Updated Sep 10, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 6 2 Updated Sep 10, 2026
View all repositories