Repositories list

• 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

  •443•1.6k•14•10•Updated Mar 9, 2026Mar 9, 2026

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  tutorialscvi-toolsscverse

  tutorialscvi-toolsscverse

  Jupyter Notebook

  •

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

  •31•63•1•4•Updated Mar 9, 2026Mar 9, 2026

• 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 Mar 9, 2026Mar 9, 2026

• rapids_singlecell

  Public

  scverse/rapids_singlecell’s past year of commit activity
  rapids_singlecell: GPU-accelerated framework for scRNA analysis

  bioinformaticsgpusingle-cell+ 2

  bioinformaticsgpusingle-cellanndatascverse

  Python

  •

  MIT License

  •42•311•15•8•Updated Mar 9, 2026Mar 9, 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•2•Updated Mar 9, 2026Mar 9, 2026

• cookiecutter-scverse-presentation

  Public
  Introduction to our template

  0•2•0•0•Updated Mar 9, 2026Mar 9, 2026

• cookiecutter-scverse

  Public

  scverse/cookiecutter-scverse’s past year of commit activity
  Cookiecutter template for scverse

  Python

  •

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

  •17•89•22•3•Updated Mar 9, 2026Mar 9, 2026

• governance

  Public

  scverse/governance’s past year of commit activity
  Governance docs for scverse

  governancescverse

  governancescverse

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

  •0•7•15•0•Updated Mar 9, 2026Mar 9, 2026

• prelude-runner

  Public

  scverse/prelude-runner’s past year of commit activity
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•1•1•0•Updated Mar 9, 2026Mar 9, 2026

• session-info2

  Public

  scverse/session-info2’s past year of commit activity
  Python

  •

  Mozilla Public License 2.0

  •1•7•1•0•Updated Mar 9, 2026Mar 9, 2026

• ecosystem-packages

  Public

  scverse/ecosystem-packages’s past year of commit activity
  Registry for scverse ecosystem packages

  Python

  •

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

  •69•34•8•12•Updated Mar 9, 2026Mar 9, 2026

• scanpy

  Public

  scverse/scanpy’s past year of commit activity
  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

  •718•2.4k•490•78•Updated Mar 9, 2026Mar 9, 2026

• zulip-bots

  Public

  scverse/zulip-bots’s past year of commit activity
  Repository for zulip bots for scverse.zulipchat.com

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

  •0•0•0•0•Updated Mar 9, 2026Mar 9, 2026

• fast-array-utils

  Public

  scverse/fast-array-utils’s past year of commit activity
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •1•13•15•4•Updated Mar 9, 2026Mar 9, 2026

• scverse-tutorials

  Public

  scverse/scverse-tutorials’s past year of commit activity
  Tutorials for learning scverse

  Python

  •

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

  •16•19•12•5•Updated Mar 9, 2026Mar 9, 2026

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •122•235•15•1•Updated Mar 9, 2026Mar 9, 2026

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4

  data-sciencemachine-learningbioinformaticstranscriptomicsscanpyanndatascverse

  Python

  •

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

  •184•716•184•66•Updated Mar 9, 2026Mar 9, 2026

• annbatch

  Public

  scverse/annbatch’s past year of commit activity
  Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

  Python

  •

  MIT License

  •3•26•22•11•Updated Mar 9, 2026Mar 9, 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•109•9•3•Updated Mar 9, 2026Mar 9, 2026

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •13•60•13•2•Updated Mar 9, 2026Mar 9, 2026

• simple-scvi

  Public
  Simple scVI implementation

  Python

  •

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

  •5•12•0•3•Updated Mar 9, 2026Mar 9, 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 9, 2026Mar 9, 2026

• napari-spatialdata

  Public

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

  visualizationspatial-analysisnapari-plugin+ 2

  visualizationspatial-analysisnapari-pluginnaparispatial-omics

  Python

  •

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

  •22•76•68•3•Updated Mar 9, 2026Mar 9, 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 9, 2026Mar 9, 2026

• scirpy

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

  Python

  •

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

  •43•246•41•6•Updated Mar 9, 2026Mar 9, 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 9, 2026Mar 9, 2026

• spatialdata-io

  Public
  Python

  •

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

  •54•89•64•14•Updated Mar 9, 2026Mar 9, 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

  •108•553•64•25•Updated Mar 9, 2026Mar 9, 2026

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •18•74•78•9•Updated Mar 9, 2026Mar 9, 2026

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

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

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