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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 791

  2. anndata anndata Public

    Annotated data.

    Python 776 218

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 478

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 603 123

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 400 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 347 67

Repositories

Showing 10 of 97 repositories
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 80 MIT 7 39 64 Updated Oct 9, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 603 BSD-3-Clause 123 78 (1 issue needs help) 23 Updated Oct 9, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 776 BSD-3-Clause 218 187 (4 issues need help) 94 Updated Oct 9, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 400 MIT 52 15 15 Updated Oct 9, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 3 1 Updated Oct 9, 2026
  • anndata-rs Public
    scverse/anndata-rs's past year of commit activity
    Rust 50 BSD-3-Clause 17 12 9 Updated Oct 9, 2026
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot's past year of commit activity
    Python 86 BSD-3-Clause 22 17 4 Updated Oct 9, 2026
  • spatialdata-io Public
    scverse/spatialdata-io's past year of commit activity
    Python 103 BSD-3-Clause 64 70 14 Updated Oct 9, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,581 BSD-3-Clause 791 445 (3 issues need help) 102 Updated Oct 9, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 11 BSD-3-Clause 0 37 1 Updated Oct 9, 2026
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