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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 777

  2. anndata anndata Public

    Annotated data.

    Python 770 208

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 473

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 598 121

  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 342 66

Repositories

Showing 10 of 97 repositories
  • 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 9 1 Updated Sep 13, 2026
  • liana-tutorials Public
    scverse/liana-tutorials's past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Sep 13, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 394 MIT 52 14 9 Updated Sep 12, 2026
  • SnapATAC2 Public

    Single-cell epigenomics analysis tools

    scverse/SnapATAC2's past year of commit activity
    Python 323 MIT 43 68 3 Updated Sep 12, 2026
  • acumen Public
    scverse/acumen's past year of commit activity
    Python 8 MIT 1 1 1 Updated Sep 12, 2026
  • 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 94 305 19 Updated Sep 11, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler's past year of commit activity
    Python 293 BSD-3-Clause 38 3 2 Updated Sep 11, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 196 22 40 11 Updated Sep 11, 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 4 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
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