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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 801

  2. anndata anndata Public

    Annotated data.

    Python 781 219

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 483

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 611 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 406 54

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 352 68

Repositories

Showing 10 of 100 repositories
  • sp-ops Public

    Prototype schema and APIs for OPS support in SpatialData

    scverse/sp-ops's past year of commit activity
    1 BSD-3-Clause 1 0 9 Updated Oct 23, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 611 BSD-3-Clause 128 82 (1 issue needs help) 28 Updated Oct 23, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler's past year of commit activity
    Python 300 BSD-3-Clause 39 1 2 Updated Oct 22, 2026
  • decoupler-tutorials Public
    scverse/decoupler-tutorials's past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 1 0 Updated Oct 23, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 13 BSD-3-Clause 0 30 0 Updated Oct 22, 2026
  • acumen Public

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

    scverse/acumen's past year of commit activity
    Python 18 MIT 1 2 2 Updated Oct 22, 2026
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils's past year of commit activity
    Python 15 MPL-2.0 5 17 (1 issue needs help) 6 Updated Oct 22, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,208 BSD-2-Clause 99 25 3 Updated Oct 22, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 199 24 48 13 Updated Oct 22, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 781 BSD-3-Clause 219 186 (4 issues need help) 91 Updated Oct 22, 2026
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