Repositories list

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •18•76•34•3•Updated Mar 30, 2026Mar 30, 2026

• anndataR

  Public
  AnnData interoperability in R

  interoperabilityanndatah5ad

  interoperabilityanndatah5ad

  R

  •

  Other

  •16•167•30•9•Updated Mar 30, 2026Mar 30, 2026

• annbatch

  Public
  Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

  Python

  •

  MIT License

  •3•28•22•8•Updated Mar 30, 2026Mar 30, 2026

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •17•89•24•8•Updated Mar 30, 2026Mar 30, 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 templat…

  Python

  •

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

  •6•5•0•4•Updated Mar 30, 2026Mar 30, 2026

• mudata

  Public
  Multimodal Data (.h5mu) implementation for Python

  genomicsmuondata-analysis+ 5

  genomicsmuondata-analysismulti-omicsanndatamultimodal-omics-analysismudatascverse

  Python

  •

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

  •21•111•10•5•Updated Mar 30, 2026Mar 30, 2026

• scverse-misc

  Public
  Miscellaneous utility code used by scverse packages

  Python

  •

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

  •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

• rapids-singlecell

  Public
  rapids-singlecell: GPU-accelerated framework for scRNA analysis

  bioinformaticsgpusingle-cell+ 2

  bioinformaticsgpusingle-cellanndatascverse

  Python

  •

  MIT License

  •43•341•14•10•Updated Mar 30, 2026Mar 30, 2026

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •13•60•13•2•Updated Mar 30, 2026Mar 30, 2026

• 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 Mar 30, 2026Mar 30, 2026

• napari-spatialdata

  Public
  Interactive visualization of spatial omics data

  visualizationspatial-analysisnapari-plugin+ 2

  visualizationspatial-analysisnapari-pluginnaparispatial-omics

  Python

  •

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

  •22•81•68•3•Updated Mar 30, 2026Mar 30, 2026

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

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

  •25•65•9•1•Updated Mar 30, 2026Mar 30, 2026

• cookiecutter-scverse-presentation

  Public
  Introduction to our template

  0•2•0•1•Updated Mar 30, 2026Mar 30, 2026

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  tutorialscvi-toolsscverse

  tutorialscvi-toolsscverse

  Jupyter Notebook

  •

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

  •32•64•1•5•Updated Mar 30, 2026Mar 30, 2026

• zulip-bots

  Public
  Repository for zulip bots for scverse.zulipchat.com

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

  •0•0•0•1•Updated Mar 30, 2026Mar 30, 2026

• squidpy

  Public
  Spatial Single Cell Analysis in Python

  data-visualizationspatial-analysisimage-analysis+ 4

  data-visualizationspatial-analysisimage-analysissingle-cell-genomicssingle-cell-rna-seqspatial-transcriptomicssquidpy

  Python

  •

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

  •110•558•65•24•Updated Mar 30, 2026Mar 30, 2026

• spatialdata-io

  Public
  Python

  •

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

  •55•92•66•15•Updated Mar 30, 2026Mar 30, 2026

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•1•1•1•Updated Mar 30, 2026Mar 30, 2026

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •87•358•256•14•Updated Mar 30, 2026Mar 30, 2026

• scvi-tools

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

  deep-learningscrna-seqvariational-autoencoder+ 7

  deep-learningscrna-seqvariational-autoencodervariational-bayessingle-cell-genomicssingle-cell-rna-seqdeep-generative-modelcite-seqhuman-cell-atlasscverse

  Python

  •

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

  •441•1.6k•15•12•Updated Mar 30, 2026Mar 30, 2026

• session-info2

  Public
  Python

  •

  Mozilla Public License 2.0

  •1•7•1•1•Updated Mar 30, 2026Mar 30, 2026

• ecosystem-packages

  Public
  Registry for scverse ecosystem packages

  Python

  •

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

  •72•35•8•7•Updated Mar 30, 2026Mar 30, 2026

• genomic-features

  Public
  Genomic Features in Python from BioConductor's AnnotationHub

  pythongenomics

  pythongenomics

  Python

  •

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

  •5•22•19•8•Updated Mar 30, 2026Mar 30, 2026

• scvi-colab

  Public
  Lightweight helper to install scvi-tools in Google Colab

  Python

  •

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

  •1•2•1•1•Updated Mar 30, 2026Mar 30, 2026

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •16•20•12•6•Updated Mar 30, 2026Mar 30, 2026

• formulaic-contrasts

  Public
  Build contrasts for models defined with formulaic

  Python

  •

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

  •2•12•2•2•Updated Mar 30, 2026Mar 30, 2026

• scirpy

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

  Python

  •

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

  •43•246•36•5•Updated Mar 30, 2026Mar 30, 2026

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •122•235•15•2•Updated Mar 30, 2026Mar 30, 2026

• scanpy

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

  pythondata-sciencemachine-learning+ 6

  pythondata-sciencemachine-learningbioinformaticstranscriptomicsvisualize-datascanpyanndatascverse

  Python

  •

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

  •723•2.4k•479•81•Updated Mar 30, 2026Mar 30, 2026

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •2•14•15•5•Updated Mar 30, 2026Mar 30, 2026