Repositories list

• napari-spatialdata

  Public

  scverse/napari-spatialdata’s past year of commit activity
  Interactive visualization of spatial omics data

  visualizationspatial-analysisnapari-plugin+ 2naparispatial-omics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •23•73•67•2•Updated Jan 6, 2026Jan 6, 2026

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •25•63•9•0•Updated Jan 6, 2026Jan 6, 2026

• scanpy

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

  pythondata-sciencemachine-learning+ 6bioinformaticstranscriptomicsvisualize-datascanpyanndatascverse

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •687•2.3k•485•76•Updated Jan 6, 2026Jan 6, 2026

• SnapATAC2

  Public
  Single-cell epigenomics analysis tools

  single-cell-genomics

  Python

  •

  MIT License

  •37•301•61•1•Updated Jan 6, 2026Jan 6, 2026

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •78•338•254•7•Updated Jan 6, 2026Jan 6, 2026

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •179•697•199•71•Updated Jan 5, 2026Jan 5, 2026

• cookiecutter-scverse-instance

  Public
  Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•5•0•2•Updated Jan 5, 2026Jan 5, 2026

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •15•87•21•1•Updated Jan 5, 2026Jan 5, 2026

• spatialdata-integration-testing

  Public
  Integration testing for the SpatialData framework

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Jan 3, 2026Jan 3, 2026

• ecosystem-packages

  Public
  Registry for scverse ecosystem packages

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •65•32•7•11•Updated Jan 1, 2026Jan 1, 2026

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •18•73•84•11•Updated Dec 31, 2025Dec 31, 2025

• scvi-tools

  Public
  Deep probabilistic analysis of single-cell and spatial omics data

  deep-learningscrna-seqvariational-autoencoder+ 7variational-bayessingle-cell-genomicssingle-cell-rna-seqdeep-generative-modelcite-seqhuman-cell-atlasscverse

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •430•1.5k•18•10•Updated Dec 31, 2025Dec 31, 2025

• pandas-uuid

  Public
  Pandas ExtensionArray / ExtensionDType for UUID

  Python

  •

  Mozilla Public License 2.0

  •0•1•5•0•Updated Dec 30, 2025Dec 30, 2025

• spatialdata-io

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •52•86•58•18•Updated Dec 29, 2025Dec 29, 2025

• pertpy

  Public
  Single-cell perturbation analysis

  single-cellperturbationscverse

  Python

  •

  MIT License

  •42•247•31•4•Updated Dec 27, 2025Dec 27, 2025

• decoupler

  Public
  Python package to perform enrichment analysis from omics data.

  pythondata-sciencebioinformatics+ 6enrichmentnumbatranscriptomicssingle-cellenrichment-analysisspatial-transcriptomics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •34•245•4•4•Updated Dec 23, 2025Dec 23, 2025

• rapids_singlecell

  Public
  rapids_singlecell: GPU-accelerated framework for scRNA analysis

  bioinformaticsgpusingle-cell+ 2anndatascverse

  Python

  •

  MIT License

  •39•288•19•8•Updated Dec 23, 2025Dec 23, 2025

• anndata-plot

  Public
  Python

  •

  MIT License

  •3•8•1•4•Updated Dec 22, 2025Dec 22, 2025

• cookiecutter-scverse-presentation

  Public
  Introduction to our template

  0•2•0•0•Updated Dec 22, 2025Dec 22, 2025

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •1•12•14•2•Updated Dec 22, 2025Dec 22, 2025

• scvi-colab

  Public
  Lightweight helper to install scvi-tools in Google Colab

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•2•1•0•Updated Dec 22, 2025Dec 22, 2025

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  tutorialscvi-toolsscverse

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •29•58•2•3•Updated Dec 22, 2025Dec 22, 2025

• session-info2

  Public
  Python

  •

  Mozilla Public License 2.0

  •1•7•1•0•Updated Dec 22, 2025Dec 22, 2025

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•1•1•0•Updated Dec 22, 2025Dec 22, 2025

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •120•231•15•1•Updated Dec 22, 2025Dec 22, 2025

• zulip-bots

  Public
  Repository for zulip bots for scverse.zulipchat.com

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 22, 2025Dec 22, 2025

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •15•18•12•5•Updated Dec 22, 2025Dec 22, 2025

• plotting_api

  Public
  Experimenting with a simplified plotting API for scanpy/scirpy

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•3•2•Updated Dec 22, 2025Dec 22, 2025

• squidpy

  Public
  Spatial Single Cell Analysis in Python

  data-visualizationspatial-analysisimage-analysis+ 4single-cell-genomicssingle-cell-rna-seqspatial-transcriptomicssquidpy

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •101•546•74•17•Updated Dec 22, 2025Dec 22, 2025

• genomic-features

  Public
  Genomic Features in Python from BioConductor's AnnotationHub

  pythongenomics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5•22•19•8•Updated Dec 22, 2025Dec 22, 2025