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

  •366•1.3k•45•10•Updated Jan 12, 2025Jan 12, 2025

• pertpy

  Public
  Perturbation Analysis in the scverse ecosystem.

  single-cellperturbationscverse

  Python

  •

  MIT License

  •23•147•34•2•Updated Jan 10, 2025Jan 10, 2025

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

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

  •157•592•194•52•Updated Jan 10, 2025Jan 10, 2025

• scanpy

  Public
  Single-cell analysis in Python. Scales to >1M cells.

  data-sciencemachine-learningbioinformatics+ 6transcriptomicsvisualize-datascanpyanndatascversepython

  Python

  •

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

  •608•2k•509•71•Updated Jan 10, 2025Jan 10, 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

  •85•453•71•8•Updated Jan 10, 2025Jan 10, 2025

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •14•39•61•5•Updated Jan 8, 2025Jan 8, 2025

• scverse.github.io

  Public
  scverse.org website

  SCSS

  •6•1•17•2•Updated Jan 8, 2025Jan 8, 2025

• ecosystem-packages

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

  Python

  •

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

  •40•19•6•6•Updated Jan 7, 2025Jan 7, 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•2•Updated Jan 7, 2025Jan 7, 2025

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •10•72•20•1•Updated Jan 7, 2025Jan 7, 2025

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •117•194•16•2•Updated Jan 7, 2025Jan 7, 2025

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •13•14•13•5•Updated Jan 7, 2025Jan 7, 2025

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•0•1•0•Updated Jan 7, 2025Jan 7, 2025

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  scvi-toolsscversetutorial

  Jupyter Notebook

  •

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

  •25•48•8•6•Updated Jan 7, 2025Jan 7, 2025

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

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

  •19•39•5•2•Updated Jan 7, 2025Jan 7, 2025

• spatialdata-io

  Public
  Python

  •

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

  •29•45•44•12•Updated Jan 6, 2025Jan 6, 2025

• scirpy

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

  Python

  •

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

  •36•223•39•6•Updated Jan 6, 2025Jan 6, 2025

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •8•42•11•1•Updated Jan 6, 2025Jan 6, 2025

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •47•247•176•12•Updated Jan 6, 2025Jan 6, 2025

• napari-spatialdata

  Public
  Interactive visualization of spatial omics data

  visualizationspatial-analysisnapari-plugin+ 2naparispatial-omics

  Python

  •

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

  •17•45•52•2•Updated Jan 6, 2025Jan 6, 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

  •23•163•14•4•Updated Jan 6, 2025Jan 6, 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 Jan 6, 2025Jan 6, 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 Jan 6, 2025Jan 6, 2025

• formulaic-contrasts

  Public
  Build contrasts for models defined with formulaic

  Python

  •

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

  •1•10•2•1•Updated Jan 6, 2025Jan 6, 2025

• anndataR

  Public
  AnnData interoperability in R

  anndatah5ad

  R

  •

  Other

  •11•67•21•5•Updated Jan 6, 2025Jan 6, 2025

• spatialdata-basel-workshop-2024

  Public
  TeX

  •1•0•0•0•Updated Jan 4, 2025Jan 4, 2025

• pertpy-tutorials

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •9•5•0•0•Updated Jan 4, 2025Jan 4, 2025

• rapids_singlecell-notebooks

  Public
  Jupyter Notebook

  •

  MIT License

  •1•4•0•0•Updated Dec 30, 2024Dec 30, 2024

• cookiecutter-scverse-presentation

  Public
  Introduction to our template

  0•0•0•0•Updated Dec 26, 2024Dec 26, 2024

• simple-scvi

  Public
  Simple scVI implementation

  Python

  •

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

  •4•10•0•2•Updated Dec 23, 2024Dec 23, 2024