Repositories list

• scverse.github.io

  Public
  scverse.org website

  SCSS

  •9•3•17•1•Updated Feb 22, 2026Feb 22, 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

  •441•1.6k•16•12•Updated Feb 22, 2026Feb 22, 2026

• anndataR

  Public
  AnnData interoperability in R

  anndatah5ad

  R

  •

  Other

  •16•152•30•9•Updated Feb 21, 2026Feb 21, 2026

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  Python

  •

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

  •81•351•253•9•Updated Feb 21, 2026Feb 21, 2026

• rapids_singlecell

  Public
  rapids_singlecell: GPU-accelerated framework for scRNA analysis

  bioinformaticsgpusingle-cell+ 2anndatascverse

  Python

  •

  MIT License

  •41•300•13•6•Updated Feb 20, 2026Feb 20, 2026

• scanpy

  Public
  Single-cell analysis in Python. Scales to >100M cells.

  pythondata-sciencemachine-learning+ 6bioinformaticstranscriptomicsvisualize-datascanpyanndatascverse

  Python

  •

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

  •715•2.4k•488•76•Updated Feb 20, 2026Feb 20, 2026

• 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

  •106•552•78•19•Updated Feb 20, 2026Feb 20, 2026

• anndata

  Public

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

  data-sciencemachine-learningbioinformatics+ 4transcriptomicsscanpyanndatascverse

  Python

  •

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

  •182•712•184•64•Updated Feb 20, 2026Feb 20, 2026

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •18•73•85•9•Updated Feb 19, 2026Feb 19, 2026

• 2026_hackathon_morphology

  Public
  0•0•0•0•Updated Feb 19, 2026Feb 19, 2026

• spatialdata-io

  Public
  Python

  •

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

  •52•88•62•13•Updated Feb 18, 2026Feb 18, 2026

• pertpy

  Public
  Single-cell perturbation analysis

  single-cellperturbationscverse

  Python

  •

  MIT License

  •48•286•29•4•Updated Feb 18, 2026Feb 18, 2026

• annbatch

  Public
  Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

  Python

  •

  MIT License

  •3•24•22•11•Updated Feb 17, 2026Feb 17, 2026

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  tutorialscvi-toolsscverse

  Jupyter Notebook

  •

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

  •30•62•2•4•Updated Feb 17, 2026Feb 17, 2026

• scvi-colab

  Public
  Lightweight helper to install scvi-tools in Google Colab

  Python

  •

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

  •1•2•1•0•Updated Feb 17, 2026Feb 17, 2026

• scirpy

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

  Python

  •

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

  •42•245•40•5•Updated Feb 17, 2026Feb 17, 2026

• 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 templat…

  Python

  •

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

  •6•5•0•2•Updated Feb 16, 2026Feb 16, 2026

• cookiecutter-scverse

  Public
  Cookiecutter template for scverse

  Python

  •

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

  •16•88•22•1•Updated Feb 16, 2026Feb 16, 2026

• session-info2

  Public
  Python

  •

  Mozilla Public License 2.0

  •1•7•1•0•Updated Feb 16, 2026Feb 16, 2026

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •0•1•1•0•Updated Feb 16, 2026Feb 16, 2026

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •1•13•15•3•Updated Feb 16, 2026Feb 16, 2026

• mudata

  Public
  Multimodal Data (.h5mu) implementation for Python

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

  Python

  •

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

  •21•108•9•2•Updated Feb 16, 2026Feb 16, 2026

• cookiecutter-scverse-presentation

  Public
  Introduction to our template

  0•2•0•0•Updated Feb 16, 2026Feb 16, 2026

• anndata-plot

  Public
  Python

  •

  MIT License

  •3•8•1•4•Updated Feb 16, 2026Feb 16, 2026

• zulip-bots

  Public
  Repository for zulip bots for scverse.zulipchat.com

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

  •0•0•0•0•Updated Feb 16, 2026Feb 16, 2026

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •16•19•12•5•Updated Feb 16, 2026Feb 16, 2026

• ecosystem-packages

  Public
  Registry for scverse ecosystem packages

  Python

  •

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

  •69•34•8•14•Updated Feb 16, 2026Feb 16, 2026

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •122•234•15•1•Updated Feb 16, 2026Feb 16, 2026

• 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 Feb 16, 2026Feb 16, 2026

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •13•59•13•2•Updated Feb 16, 2026Feb 16, 2026