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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 784

  2. anndata anndata Public

    Annotated data.

    Python 775 214

  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 398 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 347 67

Repositories

Showing 10 of 97 repositories
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,202 BSD-2-Clause 97 26 17 Updated Oct 1, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,578 BSD-3-Clause 784 443 (3 issues need help) 101 Updated Oct 1, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 775 BSD-3-Clause 214 187 (4 issues need help) 90 Updated Sep 30, 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 Sep 30, 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 11 Updated Sep 30, 2026
  • acumen Public

    A toolkit to test, validate, and improve agentic skills.

    scverse/acumen's past year of commit activity
    Python 10 MIT 1 2 2 Updated Sep 30, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 398 MIT 52 12 9 Updated Sep 30, 2026
  • scirpy Public

    A scanpy extension to analyse single-cell TCR and BCR data.

    scverse/scirpy's past year of commit activity
    Python 266 BSD-3-Clause 50 35 (2 issues need help) 11 Updated Sep 30, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy's past year of commit activity
    Python 347 MIT 67 9 4 Updated Sep 30, 2026
  • session-info2 Public
    scverse/session-info2's past year of commit activity
    Python 9 MPL-2.0 2 1 0 Updated Sep 30, 2026
View all repositories