Repositories list

• scirpy

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

  Python

  •

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

  •41•241•37•4•Updated Oct 19, 2025Oct 19, 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

  •413•1.5k•22•3•Updated Oct 19, 2025Oct 19, 2025

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

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

  •175•665•210•61•Updated Oct 19, 2025Oct 19, 2025

• ecosystem-packages

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

  Python

  •

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

  •58•29•6•10•Updated Oct 17, 2025Oct 17, 2025

• anndataR

  Public
  AnnData interoperability in R

  anndatah5ad

  R

  •

  Other

  •14•119•25•4•Updated Oct 17, 2025Oct 17, 2025

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •1•11•17•3•Updated Oct 17, 2025Oct 17, 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

  •98•522•80•17•Updated Oct 16, 2025Oct 16, 2025

• scanpy

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

  pythondata-sciencemachine-learning+ 6bioinformaticstranscriptomicsvisualize-datascanpyanndatascverse

  Python

  •

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

  •673•2.2k•500•78•Updated Oct 16, 2025Oct 16, 2025

• annbatch

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

  Python

  •

  MIT License

  •1•9•11•7•Updated Oct 15, 2025Oct 15, 2025

• Muon.jl

  Public
  Muon for Julia

  juliamuonomics+ 5single-cellmulti-omicsanndatamudatascverse

  Julia

  •

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

  •6•27•1•0•Updated Oct 15, 2025Oct 15, 2025

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  tutorialscvi-toolsscverse

  Jupyter Notebook

  •

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

  •30•55•6•2•Updated Oct 15, 2025Oct 15, 2025

• 202510_workshop_GSCN

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Oct 14, 2025Oct 14, 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

  •4•4•0•1•Updated Oct 14, 2025Oct 14, 2025

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •14•83•21•0•Updated Oct 14, 2025Oct 14, 2025

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •15•18•11•6•Updated Oct 14, 2025Oct 14, 2025

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •120•225•15•2•Updated Oct 14, 2025Oct 14, 2025

• session-info2

  Public
  Python

  •

  Mozilla Public License 2.0

  •1•7•1•0•Updated Oct 14, 2025Oct 14, 2025

• anndata-plot

  Public
  Python

  •

  MIT License

  •3•9•1•3•Updated Oct 14, 2025Oct 14, 2025

• rapids_singlecell

  Public
  rapids_singlecell: GPU-accelerated framework for scRNA analysis

  bioinformaticsgpusingle-cell+ 2anndatascverse

  Python

  •

  MIT License

  •34•246•24•12•Updated Oct 14, 2025Oct 14, 2025

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•1•1•0•Updated Oct 13, 2025Oct 13, 2025

• pertpy

  Public
  Single-cell perturbation analysis

  single-cellperturbationscverse

  Python

  •

  MIT License

  •36•204•29•3•Updated Oct 13, 2025Oct 13, 2025

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

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

  •26•60•8•4•Updated Oct 13, 2025Oct 13, 2025

• simple-scvi

  Public
  Simple scVI implementation

  Python

  •

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

  •4•12•0•3•Updated Oct 13, 2025Oct 13, 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 Oct 13, 2025Oct 13, 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 Oct 13, 2025Oct 13, 2025

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •17•68•96•11•Updated Oct 13, 2025Oct 13, 2025

• spatialdata-io

  Public
  Python

  •

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

  •47•73•56•19•Updated Oct 13, 2025Oct 13, 2025

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •71•318•237•18•Updated Oct 13, 2025Oct 13, 2025

• formulaic-contrasts

  Public
  Build contrasts for models defined with formulaic

  Python

  •

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

  •2•13•2•3•Updated Oct 13, 2025Oct 13, 2025

• 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 Oct 13, 2025Oct 13, 2025