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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 808

  2. anndata anndata Public

    Annotated data.

    Python 784 220

  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 612 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 408 55

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 355 69

Repositories

Showing 10 of 103 repositories
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 408 MIT 55 15 16 Updated Oct 30, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 134 BSD-3-Clause 28 9 2 Updated Oct 30, 2026
  • pytometry Public

    Flow & mass cytometry analytics.

    scverse/pytometry's past year of commit activity
    Python 61 Apache-2.0 15 12 (2 issues need help) 3 Updated Oct 30, 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 Oct 30, 2026
  • cupy-stubs Public

    Type stubs for CuPy

    scverse/cupy-stubs's past year of commit activity
    Python 4 MPL-2.0 0 1 0 Updated Oct 30, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 612 BSD-3-Clause 128 82 (1 issue needs help) 25 Updated Oct 30, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,720 BSD-3-Clause 482 14 (1 issue needs help) 14 Updated Oct 30, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,599 BSD-3-Clause 808 453 (3 issues need help) 114 Updated Oct 30, 2026
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils's past year of commit activity
    Python 15 MPL-2.0 6 17 (1 issue needs help) 4 Updated Oct 30, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,209 BSD-2-Clause 97 25 3 Updated Oct 29, 2026
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