Repositories list

• anndata

  Public
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

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

  •154•577•192•58•Updated Nov 14, 2024Nov 14, 2024

• 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

  •81•440•61•5•Updated Nov 14, 2024Nov 14, 2024

• anndataR

  Public
  AnnData interoperability in R

  anndatah5ad

  R

  •

  Other

  •11•58•21•13•Updated Nov 14, 2024Nov 14, 2024

• scanpy

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

  data-sciencemachine-learningbioinformatics+ 6transcriptomicsvisualize-datascanpyanndatascversepython

  Python

  •

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

  •602•1.9k•509•75•Updated Nov 14, 2024Nov 14, 2024

• 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

  •22•149•13•4•Updated Nov 14, 2024Nov 14, 2024

• 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

  •351•1.2k•49•14•Updated Nov 14, 2024Nov 14, 2024

• scirpy

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

  Python

  •

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

  •34•220•39•5•Updated Nov 14, 2024Nov 14, 2024

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •45•236•179•18•Updated Nov 13, 2024Nov 13, 2024

• pertpy-datasets

  Public
  Dataset preparation for pertpy

  Jupyter Notebook

  •

  MIT License

  •1•1•1•0•Updated Nov 13, 2024Nov 13, 2024

• spatialdata-basel-workshop-2024

  Public
  0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• spatialdata-io

  Public
  Python

  •

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

  •27•42•38•15•Updated Nov 12, 2024Nov 12, 2024

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  scvi-toolsscversetutorial

  Jupyter Notebook

  •

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

  •25•46•8•6•Updated Nov 12, 2024Nov 12, 2024

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •14•35•61•8•Updated Nov 11, 2024Nov 11, 2024

• 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 Nov 11, 2024Nov 11, 2024

• 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 Nov 11, 2024Nov 11, 2024

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •9•70•19•1•Updated Nov 11, 2024Nov 11, 2024

• scverse.github.io

  Public
  scverse.org website

  SCSS

  •6•1•16•2•Updated Nov 11, 2024Nov 11, 2024

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•0•1•0•Updated Nov 11, 2024Nov 11, 2024

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •13•13•14•7•Updated Nov 11, 2024Nov 11, 2024

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •116•187•16•2•Updated Nov 11, 2024Nov 11, 2024

• spatialdata-notebooks

  Public
  Jupyter Notebook

  •

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

  •19•37•6•7•Updated Nov 11, 2024Nov 11, 2024

• napari-spatialdata

  Public
  Interactive visualization of spatial omics data

  visualizationspatial-analysisnapari-plugin+ 2naparispatial-omics

  Python

  •

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

  •17•41•50•6•Updated Nov 11, 2024Nov 11, 2024

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •9•42•12•1•Updated Nov 11, 2024Nov 11, 2024

• plotting_api

  Public
  Experimenting with a simplified plotting API for scanpy/scirpy

  Jupyter Notebook

  •

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

  •0•1•2•2•Updated Nov 11, 2024Nov 11, 2024

• genomic-features

  Public
  Genomic Features in Python from BioConductor's AnnotationHub

  genomicspython

  Python

  •

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

  •5•19•19•7•Updated Nov 11, 2024Nov 11, 2024

• squidpy_notebooks

  Public
  Tutorials for Squidpy

  Jupyter Notebook

  •

  MIT License

  •17•30•6•2•Updated Nov 7, 2024Nov 7, 2024

• integration-testing

  Public
  A repo for integration testing core packages against upstream core packages

  MIT License

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• muon

  Public
  muon is a multimodal omics Python framework

  muonscrna-seqmulti-omics+ 8multimodal-datacite-seqscanpyscatac-seqanndatamultimodal-omics-analysismudata+ 1

  Python

  •

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

  •31•218•36•4•Updated Oct 30, 2024Oct 30, 2024

• simple-scvi

  Public
  Simple scVI implementation

  Python

  •

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

  •4•9•0•2•Updated Oct 28, 2024Oct 28, 2024

• pertpy

  Public
  Perturbation Analysis in the scverse ecosystem.

  single-cellperturbationscverse

  Python

  •

  MIT License

  •21•141•34•1•Updated Oct 26, 2024Oct 26, 2024