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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 809

  2. anndata anndata Public

    Annotated data.

    Python 784 221

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 481

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 613 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 409 56

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 355 70

Repositories

Showing 10 of 106 repositories
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 14 BSD-3-Clause 0 42 3 Updated Nov 2, 2026
  • 202611_workshop_SBI2 Public

    Materials for the scverse workshop at SBI2 2026: deep learning on morphology data

    scverse/202611_workshop_SBI2's past year of commit activity
    Jupyter Notebook 0 0 0 1 Updated Nov 2, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 409 MIT 56 13 13 Updated Nov 1, 2026
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 92 MIT 9 32 23 Updated Nov 1, 2026
  • stats Public

    scverse statistics

    scverse/stats's past year of commit activity
    TypeScript 4 MIT 0 9 4 Updated Nov 1, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,719 BSD-3-Clause 481 13 (1 issue needs help) 13 Updated Nov 1, 2026
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials's past year of commit activity
    Jupyter Notebook 65 BSD-3-Clause 35 0 5 Updated Nov 1, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 5 2 Updated Nov 1, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages's past year of commit activity
    Python 42 BSD-3-Clause 98 7 23 Updated Nov 1, 2026
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 5 0 Updated Nov 1, 2026
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