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scverse

Foundational tools for omics data in the life sciences
README.md

scverse

Welcome to 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 2.3k 691

  2. anndata anndata Public

    Annotated data.

    Python 699 180

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.5k 434

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 547 101

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 338 79

  6. scirpy scirpy Public

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

    Python 244 41

Repositories

Showing 10 of 71 repositories
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 289 MIT 40 19 9 Updated Jan 13, 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 22 MIT 3 20 6 Updated Jan 13, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,318 BSD-3-Clause 691 488 (5 issues need help) 74 Updated Jan 13, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,534 BSD-3-Clause 434 18 (1 issue needs help) 10 Updated Jan 13, 2026
  • scirpy Public

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

    scverse/scirpy’s past year of commit activity
    Python 244 BSD-3-Clause 41 38 (3 issues need help) 4 Updated Jan 13, 2026
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 12 MPL-2.0 1 14 (1 issue needs help) 3 Updated Jan 13, 2026
  • PyDESeq2 Public

    A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

    scverse/PyDESeq2’s past year of commit activity
    Python 714 MIT 81 41 7 Updated Jan 13, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 139 16 32 12 Updated Jan 13, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 3 9 17 1 Updated Jan 12, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 32 BSD-3-Clause 66 7 12 Updated Jan 12, 2026
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