Repositories list

• scirpy

  Public

  scverse/scirpy’s past year of commit activity
  A scanpy extension to analyse single-cell TCR and BCR data.

  Python

  •

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

  •42•245•41•6•Updated Feb 2, 2026Feb 2, 2026

• ecosystem-packages

  Public

  scverse/ecosystem-packages’s past year of commit activity
  Registry for scverse ecosystem packages

  Python

  •

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

  •68•32•7•14•Updated Feb 2, 2026Feb 2, 2026

• pytometry

  Public

  scverse/pytometry’s past year of commit activity
  Flow & mass cytometry analytics.

  Python

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  Apache License 2.0

  •13•58•12•2•Updated Feb 2, 2026Feb 2, 2026

• cookiecutter-scverse

  Public

  scverse/cookiecutter-scverse’s past year of commit activity
  Cookiecutter template for scverse

  Python

  •

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

  •15•87•21•2•Updated Feb 2, 2026Feb 2, 2026

• session-info2

  Public

  scverse/session-info2’s past year of commit activity
  Python

  •

  Mozilla Public License 2.0

  •1•7•1•1•Updated Feb 2, 2026Feb 2, 2026

• squidpy

  Public

  scverse/squidpy’s past year of commit activity
  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

  •104•550•79•20•Updated Feb 2, 2026Feb 2, 2026

• scverse-tutorials

  Public

  scverse/scverse-tutorials’s past year of commit activity
  Tutorials for learning scverse

  Python

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

  •15•19•12•6•Updated Feb 2, 2026Feb 2, 2026

• scanpy-tutorials

  Public

  scverse/scanpy-tutorials’s past year of commit activity
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •120•234•15•2•Updated Feb 2, 2026Feb 2, 2026

• fast-array-utils

  Public

  scverse/fast-array-utils’s past year of commit activity
  Fast array utilities

  Python

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  Mozilla Public License 2.0

  •1•13•15•4•Updated Feb 2, 2026Feb 2, 2026

• anndata-plot

  Public

  scverse/anndata-plot’s past year of commit activity
  Python

  •

  MIT License

  •3•8•1•5•Updated Feb 2, 2026Feb 2, 2026

• decoupler

  Public

  scverse/decoupler’s past year of commit activity
  Python package to perform enrichment analysis from omics data.

  pythondata-sciencebioinformatics+ 6enrichmentnumbatranscriptomicssingle-cellenrichment-analysisspatial-transcriptomics

  Python

  •

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

  •35•252•6•4•Updated Feb 2, 2026Feb 2, 2026

• mudata

  Public

  scverse/mudata’s past year of commit activity
  Multimodal Data (.h5mu) implementation for Python

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

  Python

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

  •21•106•9•2•Updated Feb 2, 2026Feb 2, 2026

• formulaic-contrasts

  Public

  scverse/formulaic-contrasts’s past year of commit activity
  Build contrasts for models defined with formulaic

  Python

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

  •2•12•2•2•Updated Feb 2, 2026Feb 2, 2026

• Muon.jl

  Public

  scverse/Muon.jl’s past year of commit activity
  Muon for Julia

  juliamuonomics+ 5single-cellmulti-omicsanndatamudatascverse

  Julia

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

  •6•28•1•1•Updated Feb 2, 2026Feb 2, 2026

• rapids_singlecell

  Public

  scverse/rapids_singlecell’s past year of commit activity
  rapids_singlecell: GPU-accelerated framework for scRNA analysis

  bioinformaticsgpusingle-cell+ 2anndatascverse

  Python

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  MIT License

  •40•295•14•6•Updated Feb 2, 2026Feb 2, 2026

• pertpy

  Public

  scverse/pertpy’s past year of commit activity
  Single-cell perturbation analysis

  single-cellperturbationscverse

  Python

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  MIT License

  •47•281•32•6•Updated Feb 2, 2026Feb 2, 2026

• annbatch

  Public

  scverse/annbatch’s past year of commit activity
  Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

  Python

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  MIT License

  •3•24•19•5•Updated Feb 2, 2026Feb 2, 2026

• anndata

  Public

  scverse/anndata’s past year of commit activity
  Annotated data.

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

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

  •181•707•198•64•Updated Feb 2, 2026Feb 2, 2026

• scvi-tools

  Public

  scverse/scvi-tools’s past year of commit activity
  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

  •435•1.6k•18•9•Updated Feb 2, 2026Feb 2, 2026

• pandas-uuid

  Public

  scverse/pandas-uuid’s past year of commit activity
  Pandas ExtensionArray / ExtensionDType for UUID

  Python

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  Mozilla Public License 2.0

  •0•2•5•2•Updated Feb 2, 2026Feb 2, 2026

• napari-spatialdata

  Public

  scverse/napari-spatialdata’s past year of commit activity
  Interactive visualization of spatial omics data

  visualizationspatial-analysisnapari-plugin+ 2naparispatial-omics

  Python

  •

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

  •23•75•67•3•Updated Feb 1, 2026Feb 1, 2026

• spatialdata

  Public

  scverse/spatialdata’s past year of commit activity
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •80•342•256•8•Updated Feb 1, 2026Feb 1, 2026

• spatialdata-integration-testing

  Public

  scverse/spatialdata-integration-testing’s past year of commit activity
  Integration testing for the SpatialData framework

  Python

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

  •0•2•0•0•Updated Feb 1, 2026Feb 1, 2026

• spatialdata-notebooks

  Public

  scverse/spatialdata-notebooks’s past year of commit activity
  Jupyter Notebook

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

  •25•65•9•0•Updated Feb 1, 2026Feb 1, 2026

• scanpy

  Public

  scverse/scanpy’s past year of commit activity
  Single-cell analysis in Python. Scales to >100M cells.

  pythondata-sciencemachine-learning+ 6bioinformaticstranscriptomicsvisualize-datascanpyanndatascverse

  Python

  •

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

  •706•2.3k•491•78•Updated Feb 1, 2026Feb 1, 2026

• SnapATAC2

  Public
  Single-cell epigenomics analysis tools

  single-cell-genomics

  Python

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  MIT License

  •37•308•59•1•Updated Feb 1, 2026Feb 1, 2026

• spatialdata-io

  Public
  Python

  •

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

  •51•88•59•10•Updated Jan 31, 2026Jan 31, 2026

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •19•73•84•10•Updated Jan 30, 2026Jan 30, 2026

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  tutorialscvi-toolsscverse

  Jupyter Notebook

  •

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

  •29•59•2•4•Updated Jan 28, 2026Jan 28, 2026

• anndataR

  Public
  AnnData interoperability in R

  anndatah5ad

  R

  •

  Other

  •16•149•29•9•Updated Jan 28, 2026Jan 28, 2026