Repositories list

• 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

  •3•3•0•2•Updated Apr 17, 2025Apr 17, 2025

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •11•75•19•2•Updated Apr 17, 2025Apr 17, 2025

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

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

  •20•53•6•0•Updated Apr 16, 2025Apr 16, 2025

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •16•52•77•10•Updated Apr 16, 2025Apr 16, 2025

• spatialdata-io

  Public
  Python

  •

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

  •33•57•46•14•Updated Apr 16, 2025Apr 16, 2025

• anndataR

  Public
  AnnData interoperability in R

  anndatah5ad

  R

  •

  Other

  •12•75•17•6•Updated Apr 16, 2025Apr 16, 2025

• pertpy

  Public
  Perturbation Analysis in the scverse ecosystem.

  single-cellperturbationscverse

  Python

  •

  MIT License

  •29•169•31•5•Updated Apr 15, 2025Apr 15, 2025

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

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

  •163•616•192•54•Updated Apr 15, 2025Apr 15, 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

  •625•2.1k•498•74•Updated Apr 15, 2025Apr 15, 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

  •26•190•15•3•Updated Apr 15, 2025Apr 15, 2025

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •0•7•11•2•Updated Apr 15, 2025Apr 15, 2025

• ecosystem-packages

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

  Python

  •

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

  •46•21•7•7•Updated Apr 15, 2025Apr 15, 2025

• scverse.github.io

  Public
  scverse.org website

  SCSS

  •7•3•17•0•Updated Apr 14, 2025Apr 14, 2025

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•1•1•0•Updated Apr 14, 2025Apr 14, 2025

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •13•16•11•6•Updated Apr 14, 2025Apr 14, 2025

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •117•211•15•1•Updated Apr 14, 2025Apr 14, 2025

• napari-spatialdata

  Public
  Interactive visualization of spatial omics data

  visualizationspatial-analysisnapari-plugin+ 2naparispatial-omics

  Python

  •

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

  •17•52•56•1•Updated Apr 14, 2025Apr 14, 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

  •95•484•84•11•Updated Apr 14, 2025Apr 14, 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 Apr 14, 2025Apr 14, 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

  •384•1.4k•39•10•Updated Apr 14, 2025Apr 14, 2025

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •59•273•207•17•Updated Apr 14, 2025Apr 14, 2025

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  scvi-toolsscversetutorial

  Jupyter Notebook

  •

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

  •28•52•8•13•Updated Apr 14, 2025Apr 14, 2025

• genomic-features

  Public
  Genomic Features in Python from BioConductor's AnnotationHub

  genomicspython

  Python

  •

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

  •6•21•19•9•Updated Apr 14, 2025Apr 14, 2025

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •10•48•12•2•Updated Apr 14, 2025Apr 14, 2025

• scirpy

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

  Python

  •

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

  •38•230•39•3•Updated Apr 14, 2025Apr 14, 2025

• formulaic-contrasts

  Public
  Build contrasts for models defined with formulaic

  Python

  •

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

  •2•12•2•3•Updated Apr 14, 2025Apr 14, 2025

• anndata-plot

  Public
  Python

  •

  MIT License

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

• pertpy-tutorials

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •9•8•0•0•Updated Apr 9, 2025Apr 9, 2025

• 202504_workshop_GSCN

  Public
  Jupyter Notebook

  •0•3•11•0•Updated Apr 8, 2025Apr 8, 2025

• anndata-tutorials

  Public
  Use cases for anndata.

  Jupyter Notebook

  •

  Other

  •13•15•1•4•Updated Apr 7, 2025Apr 7, 2025