Repositories list

• 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

  •94•478•83•8•Updated Mar 28, 2025Mar 28, 2025

• squidpy_notebooks

  Public
  Tutorials for Squidpy

  Jupyter Notebook

  •

  MIT License

  •19•32•5•5•Updated Mar 28, 2025Mar 28, 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

  •383•1.4k•38•10•Updated Mar 28, 2025Mar 28, 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

  •620•2.1k•493•73•Updated Mar 28, 2025Mar 28, 2025

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

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

  •161•613•191•52•Updated Mar 28, 2025Mar 28, 2025

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •0•6•13•2•Updated Mar 28, 2025Mar 28, 2025

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  scvi-toolsscversetutorial

  Jupyter Notebook

  •

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

  •28•52•8•11•Updated Mar 28, 2025Mar 28, 2025

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •16•49•73•7•Updated Mar 27, 2025Mar 27, 2025

• anndata-plot

  Public
  Python

  •

  MIT License

  •1•9•1•3•Updated Mar 27, 2025Mar 27, 2025

• 202504_workshop_GSCN

  Public
  0•1•17•0•Updated Mar 27, 2025Mar 27, 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

  •3•2•0•1•Updated Mar 27, 2025Mar 27, 2025

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •11•75•19•1•Updated Mar 27, 2025Mar 27, 2025

• pertpy

  Public
  Perturbation Analysis in the scverse ecosystem.

  single-cellperturbationscverse

  Python

  •

  MIT License

  •28•167•35•4•Updated Mar 27, 2025Mar 27, 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•185•15•3•Updated Mar 26, 2025Mar 26, 2025

• spatialdata-io

  Public
  Python

  •

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

  •33•55•44•14•Updated Mar 25, 2025Mar 25, 2025

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

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

  •20•52•6•1•Updated Mar 25, 2025Mar 25, 2025

• ecosystem-packages

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

  Python

  •

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

  •46•21•6•6•Updated Mar 24, 2025Mar 24, 2025

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •117•206•14•1•Updated Mar 24, 2025Mar 24, 2025

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •13•16•11•5•Updated Mar 24, 2025Mar 24, 2025

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•1•1•0•Updated Mar 24, 2025Mar 24, 2025

• scirpy

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

  Python

  •

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

  •37•227•39•5•Updated Mar 24, 2025Mar 24, 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 Mar 24, 2025Mar 24, 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•55•1•Updated Mar 24, 2025Mar 24, 2025

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •59•269•202•15•Updated Mar 24, 2025Mar 24, 2025

• genomic-features

  Public
  Genomic Features in Python from BioConductor's AnnotationHub

  genomicspython

  Python

  •

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

  •6•21•19•8•Updated Mar 24, 2025Mar 24, 2025

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •9•46•12•1•Updated Mar 24, 2025Mar 24, 2025

• formulaic-contrasts

  Public
  Build contrasts for models defined with formulaic

  Python

  •

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

  •2•12•2•2•Updated Mar 24, 2025Mar 24, 2025

• deres

  Public
  Container and visualization for differential expression (and similar) result tables

  Python

  •

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

  •0•1•6•0•Updated Mar 19, 2025Mar 19, 2025

• mudata

  Public
  Multimodal Data (.h5mu) implementation for Python

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

  Python

  •

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

  •19•91•12•2•Updated Mar 18, 2025Mar 18, 2025

• scverse.github.io

  Public
  scverse.org website

  SCSS

  •7•2•19•3•Updated Mar 17, 2025Mar 17, 2025