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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 785

  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 476

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 599 123

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 399 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 347 67

Repositories

Showing 10 of 97 repositories
  • PyDESeq2 Public

    A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

    scverse/PyDESeq2's past year of commit activity
    Python 763 MIT 90 37 18 Updated Oct 4, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 11 BSD-3-Clause 0 38 0 Updated Oct 3, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 399 MIT 52 14 10 Updated Oct 3, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 776 BSD-3-Clause 216 187 (4 issues need help) 93 Updated Oct 3, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 4 1 Updated Oct 3, 2026
  • cookiecutter-scverse-instance Public

    Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.

    scverse/cookiecutter-scverse-instance's past year of commit activity
    Python 5 BSD-3-Clause 6 0 6 Updated Oct 3, 2026
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse's past year of commit activity
    Python 90 BSD-3-Clause 18 24 4 Updated Oct 3, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,204 BSD-2-Clause 98 25 0 Updated Oct 2, 2026
  • annbatch Public

    Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

    scverse/annbatch's past year of commit activity
    Python 70 MIT 6 25 12 Updated Oct 2, 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 Oct 2, 2026
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