Repositories list

• 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

  •382•1.3k•33•8•Updated Mar 12, 2025Mar 12, 2025

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

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

  •160•607•196•56•Updated Mar 12, 2025Mar 12, 2025

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  scvi-toolsscversetutorial

  Jupyter Notebook

  •

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

  •28•51•8•9•Updated Mar 12, 2025Mar 12, 2025

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •54•260•195•6•Updated Mar 12, 2025Mar 12, 2025

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •16•47•71•7•Updated Mar 11, 2025Mar 11, 2025

• anndataR

  Public
  AnnData interoperability in R

  anndatah5ad

  R

  •

  Other

  •11•71•16•7•Updated Mar 11, 2025Mar 11, 2025

• anndata-tutorials

  Public
  Use cases for anndata.

  Jupyter Notebook

  •

  Other

  •13•13•1•4•Updated Mar 11, 2025Mar 11, 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

  •612•2k•495•73•Updated Mar 11, 2025Mar 11, 2025

• ecosystem-packages

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

  Python

  •

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

  •46•20•6•6•Updated Mar 11, 2025Mar 11, 2025

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •0•4•9•1•Updated Mar 11, 2025Mar 11, 2025

• scirpy

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

  Python

  •

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

  •37•226•38•3•Updated Mar 11, 2025Mar 11, 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

  •89•471•81•7•Updated Mar 11, 2025Mar 11, 2025

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

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

  •19•45•5•1•Updated Mar 11, 2025Mar 11, 2025

• squidpy_notebooks

  Public
  Tutorials for Squidpy

  Jupyter Notebook

  •

  MIT License

  •19•30•6•4•Updated Mar 10, 2025Mar 10, 2025

• rapids_singlecell

  Public
  Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

  bioinformaticsgpusingle-cell+ 2anndatascverse

  Python

  •

  MIT License

  •25•176•15•2•Updated Mar 10, 2025Mar 10, 2025

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•0•1•0•Updated Mar 10, 2025Mar 10, 2025

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •13•15•13•5•Updated Mar 10, 2025Mar 10, 2025

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •117•205•14•1•Updated Mar 10, 2025Mar 10, 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 Mar 10, 2025Mar 10, 2025

• napari-spatialdata

  Public
  Interactive visualization of spatial omics data

  visualizationspatial-analysisnapari-plugin+ 2naparispatial-omics

  Python

  •

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

  •17•51•53•1•Updated Mar 10, 2025Mar 10, 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 Mar 10, 2025Mar 10, 2025

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •9•45•11•1•Updated Mar 10, 2025Mar 10, 2025

• formulaic-contrasts

  Public
  Build contrasts for models defined with formulaic

  Python

  •

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

  •1•11•2•1•Updated Mar 10, 2025Mar 10, 2025

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •11•72•23•2•Updated Mar 10, 2025Mar 10, 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 9, 2025Mar 9, 2025

• 202503_hackathon_owkin

  Public
  Repository to organise the shared hackathon with Owkin in Paris

  0•0•9•0•Updated Mar 8, 2025Mar 8, 2025

• 202504_workshop_GSCN

  Public
  0•0•17•0•Updated Mar 6, 2025Mar 6, 2025

• benchmark

  Public
  Code for running benchmarks

  Rust

  •

  GNU General Public License v3.0

  •0•3•7•2•Updated Mar 5, 2025Mar 5, 2025

• mudata

  Public
  Multimodal Data (.h5mu) implementation for Python

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

  Python

  •

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

  •19•88•16•2•Updated Mar 4, 2025Mar 4, 2025

• pertpy

  Public
  Perturbation Analysis in the scverse ecosystem.

  single-cellperturbationscverse

  Python

  •

  MIT License

  •26•162•34•2•Updated Mar 4, 2025Mar 4, 2025