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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 788

  2. anndata anndata Public

    Annotated data.

    Python 776 216

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 477

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 600 124

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 400 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 347 67

Repositories

Showing 10 of 97 repositories
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 600 BSD-3-Clause 124 82 (1 issue needs help) 29 Updated Oct 6, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 400 MIT 52 14 14 Updated Oct 5, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,205 BSD-2-Clause 98 25 2 Updated Oct 5, 2026
  • spatialdata-io Public
    scverse/spatialdata-io's past year of commit activity
    Python 103 BSD-3-Clause 64 70 14 Updated Oct 5, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 11 BSD-3-Clause 0 37 0 Updated Oct 5, 2026
  • cookiecutter-scverse-presentation Public

    Introduction to our template

    scverse/cookiecutter-scverse-presentation's past year of commit activity
    2 0 0 0 Updated Oct 5, 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 Oct 5, 2026
  • pandas-uuid Public

    Pandas ExtensionArray / ExtensionDType for UUID

    scverse/pandas-uuid's past year of commit activity
    Python 2 MPL-2.0 0 5 0 Updated Oct 5, 2026
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials's past year of commit activity
    Python 22 BSD-3-Clause 18 12 7 Updated Oct 5, 2026
  • zulip-bots Public

    Repository for zulip bots for scverse.zulipchat.com

    scverse/zulip-bots's past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Oct 5, 2026
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