Repositories list

• mudata

  Public
  Multimodal Data (.h5mu) implementation for Python

  genomicsmuondata-analysis+ 5multi-omicsanndatamultimodal-omics-analysismudatascverse

  Python

  •

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

  •19•87•16•2•Updated Mar 3, 2025Mar 3, 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

  •381•1.3k•33•6•Updated Mar 2, 2025Mar 2, 2025

• scvi-colab

  Public
  Lightweight helper to install scvi-tools in Google Colab

  Python

  •

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

  •1•1•2•0•Updated Mar 2, 2025Mar 2, 2025

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  scvi-toolsscversetutorial

  Jupyter Notebook

  •

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

  •29•51•8•9•Updated Mar 2, 2025Mar 2, 2025

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •9•43•11•1•Updated Mar 1, 2025Mar 1, 2025

• ecosystem-packages

  Public
  Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

  Python

  •

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

  •45•20•6•10•Updated Mar 1, 2025Mar 1, 2025

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

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

  •160•606•198•54•Updated Feb 28, 2025Feb 28, 2025

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •0•4•8•1•Updated Feb 28, 2025Feb 28, 2025

• muon-tutorials

  Public
  Tutorials for multimodal omics data analysis

  muonmulti-omicsmudata+ 2scversesingle-cell

  Jupyter Notebook

  •

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

  •7•13•6•0•Updated Feb 28, 2025Feb 28, 2025

• anndata-tutorials

  Public
  Use cases for anndata.

  Jupyter Notebook

  •

  Other

  •13•13•1•4•Updated Feb 28, 2025Feb 28, 2025

• shadows

  Public
  Shadow objects for AnnData and MuData (experimental)

  Python

  •

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

  •0•11•7•0•Updated Feb 28, 2025Feb 28, 2025

• pertpy-datasets

  Public
  Datasets provided through pertpy

  Jupyter Notebook

  •

  MIT License

  •1•1•1•0•Updated Feb 28, 2025Feb 28, 2025

• muon

  Public
  muon is a multimodal omics Python framework

  muonscrna-seqmulti-omics+ 8multimodal-datacite-seqscanpyscatac-seqanndatamultimodal-omics-analysismudata+ 1

  Python

  •

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

  •31•226•41•5•Updated Feb 28, 2025Feb 28, 2025

• governance

  Public
  Governance docs for scverse

  governancescverse

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

  •0•7•19•2•Updated Feb 28, 2025Feb 28, 2025

• squidpy_notebooks

  Public
  Tutorials for Squidpy

  Jupyter Notebook

  •

  MIT License

  •19•30•6•3•Updated Feb 28, 2025Feb 28, 2025

• simple-scvi

  Public
  Simple scVI implementation

  Python

  •

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

  •4•10•0•2•Updated Feb 28, 2025Feb 28, 2025

• cookiecutter-scverse-presentation

  Public
  Introduction to our template

  0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• Muon.jl

  Public
  Muon for Julia

  muonomicssingle-cell+ 5multi-omicsanndatamudatascversejulia

  Julia

  •

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

  •6•27•1•0•Updated Feb 28, 2025Feb 28, 2025

• pertpy-tutorials

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •9•6•0•0•Updated Feb 28, 2025Feb 28, 2025

• integration-testing

  Public
  A repo for integration testing core packages against upstream core packages

  MIT License

  •0•0•2•0•Updated Feb 28, 2025Feb 28, 2025

• rapids_singlecell-notebooks

  Public
  Jupyter Notebook

  •

  MIT License

  •4•5•0•1•Updated Feb 28, 2025Feb 28, 2025

• napari-spatialdata

  Public
  Interactive visualization of spatial omics data

  visualizationspatial-analysisnapari-plugin+ 2naparispatial-omics

  Python

  •

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

  •17•50•53•1•Updated Feb 28, 2025Feb 28, 2025

• plotting_api

  Public
  Experimenting with a simplified plotting API for scanpy/scirpy

  Jupyter Notebook

  •

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

  •0•1•3•2•Updated Feb 28, 2025Feb 28, 2025

• formulaic-contrasts

  Public
  Build contrasts for models defined with formulaic

  Python

  •

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

  •1•11•2•0•Updated Feb 28, 2025Feb 28, 2025

• genomic-features

  Public
  Genomic Features in Python from BioConductor's AnnotationHub

  genomicspython

  Python

  •

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

  •6•20•19•8•Updated Feb 28, 2025Feb 28, 2025

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •117•202•15•1•Updated Feb 28, 2025Feb 28, 2025

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •13•15•13•5•Updated Feb 28, 2025Feb 28, 2025

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •10•72•22•0•Updated Feb 28, 2025Feb 28, 2025

• 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

  •2•1•0•1•Updated Feb 28, 2025Feb 28, 2025

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •16•46•71•7•Updated Feb 28, 2025Feb 28, 2025