Repositories list

• anndata

  Public

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

  data-sciencemachine-learningbioinformatics+ 4

  data-sciencemachine-learningbioinformaticstranscriptomicsscanpyanndatascverse

  Python

  •

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

  •189189 forks•732732 stars•189189 issues•6969 pull requests•Updated Apr 20, 2026Apr 20, 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+ 7

  deep-learningscrna-seqvariational-autoencodervariational-bayessingle-cell-genomicssingle-cell-rna-seqdeep-generative-modelcite-seqhuman-cell-atlasscverse

  Python

  •

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

  •446446 forks•1.6k1.6k stars•1616 issues•1111 pull requests•Updated Apr 19, 2026Apr 19, 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

  •

  MIT License

  •33 forks•5252 stars•2626 issues•99 pull requests•Updated Apr 19, 2026Apr 19, 2026

• morphology2026

  Public
  SCSS

  •00 forks•33 stars•00 issues•00 pull requests•Updated Apr 18, 2026Apr 18, 2026

• scirpy

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

  Python

  •

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

  •4444 forks•247247 stars•3939 issues•77 pull requests•Updated Apr 18, 2026Apr 18, 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

  •66 forks•55 stars•00 issues•33 pull requests•Updated Apr 18, 2026Apr 18, 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

  •1717 forks•9090 stars•2424 issues•55 pull requests•Updated Apr 18, 2026Apr 18, 2026

• scverse.github.io

  Public

  scverse/scverse.github.io’s past year of commit activity
  scverse.org website

  SCSS

  •99 forks•33 stars•1515 issues•11 pull request•Updated Apr 18, 2026Apr 18, 2026

• event-template

  Public template

  scverse/event-template’s past year of commit activity
  SCSS

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• scanpy

  Public

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

  pythondata-sciencemachine-learning+ 6

  pythondata-sciencemachine-learningbioinformaticstranscriptomicsvisualize-datascanpyanndatascverse

  Python

  •

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

  •736736 forks•2.4k2.4k stars•480480 issues•8383 pull requests•Updated Apr 17, 2026Apr 17, 2026

• 2026_04_hackathon_padua

  Public
  Repository to organize and share code for the scverse Padua Hackathon, April 2026

  Jupyter Notebook

  •00 forks•33 stars•3737 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• mudata

  Public
  Multimodal Data (.h5mu) implementation for Python

  genomicsmuondata-analysis+ 5

  genomicsmuondata-analysismulti-omicsanndatamultimodal-omics-analysismudatascverse

  Python

  •

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

  •2222 forks•117117 stars•1111 issues•33 pull requests•Updated Apr 17, 2026Apr 17, 2026

• spatialdata-plot

  Public
  Static plotting for spatialdata

  Python

  •

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

  •2020 forks•7878 stars•2323 issues•44 pull requests•Updated Apr 16, 2026Apr 16, 2026

• squidpy

  Public
  Spatial Single Cell Analysis in Python

  data-visualizationspatial-analysisimage-analysis+ 4

  data-visualizationspatial-analysisimage-analysissingle-cell-genomicssingle-cell-rna-seqspatial-transcriptomicssquidpy

  Python

  •

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

  •113113 forks•562562 stars•6969 issues•2929 pull requests•Updated Apr 16, 2026Apr 16, 2026

• scverse-misc

  Public
  Miscellaneous utility code used by scverse packages

  Python

  •

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

  •00 forks•44 stars•44 issues•22 pull requests•Updated Apr 16, 2026Apr 16, 2026

• anndataR

  Public
  AnnData interoperability in R

  interoperabilityanndatah5ad

  interoperabilityanndatah5ad

  R

  •

  Other

  •1616 forks•168168 stars•3232 issues•88 pull requests•Updated Apr 16, 2026Apr 16, 2026

• rapids-singlecell

  Public
  rapids-singlecell: GPU-accelerated framework for scRNA analysis

  bioinformaticsgpusingle-cell+ 2

  bioinformaticsgpusingle-cellanndatascverse

  Python

  •

  MIT License

  •4343 forks•355355 stars•1313 issues•88 pull requests•Updated Apr 15, 2026Apr 15, 2026

• ecosystem-packages

  Public
  Registry for scverse ecosystem packages

  Python

  •

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

  •7474 forks•3636 stars•77 issues•88 pull requests•Updated Apr 15, 2026Apr 15, 2026

• decoupler

  Public
  Python package to perform enrichment analysis from omics data.

  pythondata-sciencebioinformatics+ 6

  pythondata-sciencebioinformaticsenrichmentnumbatranscriptomicssingle-cellenrichment-analysisspatial-transcriptomics

  Python

  •

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

  •3535 forks•266266 stars•44 issues•11 pull request•Updated Apr 14, 2026Apr 14, 2026

• session-info2

  Public
  Python

  •

  Mozilla Public License 2.0

  •22 forks•77 stars•11 issue•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• fast-array-utils

  Public
  Fast array utilities

  Python

  •

  Mozilla Public License 2.0

  •33 forks•1414 stars•1515 issues•44 pull requests•Updated Apr 14, 2026Apr 14, 2026

• PyDESeq2

  Public
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

  pythonbioinformaticsrna-seq+ 2

  pythonbioinformaticsrna-seqtranscriptomicsdifferential-expression

  Python

  •

  MIT License

  •8282 forks•747747 stars•4040 issues•99 pull requests•Updated Apr 14, 2026Apr 14, 2026

• cookiecutter-scverse-presentation

  Public
  Introduction to our template

  00 forks•22 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• anndata-plot

  Public
  Python

  •

  MIT License

  •33 forks•88 stars•11 issue•44 pull requests•Updated Apr 14, 2026Apr 14, 2026

• prelude-runner

  Public
  Jupyter notebook runner that executes preludes before each cell

  Python

  •

  Apache License 2.0

  •00 forks•11 star•11 issue•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •1616 forks•2020 stars•1212 issues•55 pull requests•Updated Apr 14, 2026Apr 14, 2026

• scanpy-tutorials

  Public
  Scanpy Tutorials.

  Jupyter Notebook

  •

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

  •122122 forks•235235 stars•1515 issues•11 pull request•Updated Apr 14, 2026Apr 14, 2026

• zulip-bots

  Public
  Repository for zulip bots for scverse.zulipchat.com

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  tutorialscvi-toolsscverse

  tutorialscvi-toolsscverse

  Jupyter Notebook

  •

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

  •3232 forks•6464 stars•11 issue•44 pull requests•Updated Apr 14, 2026Apr 14, 2026

• scvi-colab

  Public
  Lightweight helper to install scvi-tools in Google Colab

  Python

  •

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

  •11 fork•22 stars•11 issue•00 pull requests•Updated Apr 14, 2026Apr 14, 2026