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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 2.4k 738

  2. anndata anndata Public

    Annotated data.

    Python 732 189

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 447

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 563 113

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 362 87

  6. scirpy scirpy Public

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

    Python 247 45

Repositories

Showing 10 of 80 repositories
  • antibody-based-spatial-proteomics-guide Public

    Guide for common steps in analyzing antiboy-based spatial proteomics data, part of the scverse proteomics consortium.

    scverse/antibody-based-spatial-proteomics-guide’s past year of commit activity
    3 BSD-3-Clause 0 0 0 Updated Apr 22, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 732 BSD-3-Clause 189 189 (4 issues need help) 73 Updated Apr 22, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 3 9 15 1 Updated Apr 22, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 36 BSD-3-Clause 74 7 8 Updated Apr 22, 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 53 MIT 3 26 10 Updated Apr 22, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,602 BSD-3-Clause 447 16 (1 issue needs help) 13 Updated Apr 22, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,427 BSD-3-Clause 738 479 (4 issues need help) 85 Updated Apr 22, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy’s past year of commit activity
    Python 308 MIT 56 32 5 Updated Apr 22, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler’s past year of commit activity
    Python 266 BSD-3-Clause 35 1 1 Updated Apr 21, 2026
  • PyDESeq2 Public

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

    scverse/PyDESeq2’s past year of commit activity
    Python 747 MIT 83 39 10 Updated Apr 21, 2026
View all repositories

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