Repositories list

• 202611_workshop_SBI2

  Public
  Materials for the scverse workshop at SBI2 2026: deep learning on morphology data

  00 forks in scverse/202611_workshop_SBI2•00 stars in scverse/202611_workshop_SBI2•00 issues in scverse/202611_workshop_SBI2•00 pull requests in scverse/202611_workshop_SBI2•Updated Oct 29, 2026Oct 29, 2026

• sbi2_2026

  Public
  Landing page for the scverse workshop at SBI2 2026

  SCSS

  •00 forks in scverse/sbi2_2026•00 stars in scverse/sbi2_2026•00 issues in scverse/sbi2_2026•00 pull requests in scverse/sbi2_2026•Updated Oct 29, 2026Oct 29, 2026

• 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

  •220220 forks in scverse/anndata•783783 stars in scverse/anndata•190190 issues in scverse/anndata•9292 pull requests in scverse/anndata•Updated Oct 28, 2026Oct 28, 2026

• rustar-aligner

  Public

  scverse/rustar-aligner’s past year of commit activity
  A rust implementation of STAR

  Rust

  •

  MIT License

  •99 forks in scverse/rustar-aligner•9090 stars in scverse/rustar-aligner•3232 issues in scverse/rustar-aligner•1717 pull requests in scverse/rustar-aligner•Updated Oct 28, 2026Oct 28, 2026

• mantispy

  Public

  scverse/mantispy’s past year of commit activity
  Analysis framework for morphological profiling data

  Python

  •

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

  •00 forks in scverse/mantispy•1414 stars in scverse/mantispy•3232 issues in scverse/mantispy•22 pull requests in scverse/mantispy•Updated Oct 28, 2026Oct 28, 2026

• rapids-singlecell

  Public

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

  bioinformaticsgpusingle-cell+ 2

  bioinformaticsgpusingle-cellanndatascverse

  Python

  •

  MIT License

  •5555 forks in scverse/rapids-singlecell•408408 stars in scverse/rapids-singlecell•1515 issues in scverse/rapids-singlecell•1414 pull requests in scverse/rapids-singlecell•Updated Oct 28, 2026Oct 28, 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

  •483483 forks in scverse/scvi-tools•1.7k1.7k stars in scverse/scvi-tools•1313 issues in scverse/scvi-tools•1313 pull requests in scverse/scvi-tools•Updated Oct 28, 2026Oct 28, 2026

• anndataR

  Public

  scverse/anndataR’s past year of commit activity
  AnnData interoperability in R

  interoperabilityanndatah5ad

  interoperabilityanndatah5ad

  R

  •

  Other

  •2424 forks in scverse/anndataR•201201 stars in scverse/anndataR•5050 issues in scverse/anndataR•1010 pull requests in scverse/anndataR•Updated Oct 28, 2026Oct 28, 2026

• anndata-rs

  Public

  scverse/anndata-rs’s past year of commit activity
  Rust

  •

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

  •1515 forks in scverse/anndata-rs•5151 stars in scverse/anndata-rs•1212 issues in scverse/anndata-rs•22 pull requests in scverse/anndata-rs•Updated Oct 28, 2026Oct 28, 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

  •66 forks in scverse/annbatch•7272 stars in scverse/annbatch•2323 issues in scverse/annbatch•1010 pull requests in scverse/annbatch•Updated Oct 28, 2026Oct 28, 2026

• benchmark

  Public

  scverse/benchmark’s past year of commit activity
  Code for running benchmarks

  Rust

  •

  GNU General Public License v3.0

  •00 forks in scverse/benchmark•44 stars in scverse/benchmark•77 issues in scverse/benchmark•11 pull request in scverse/benchmark•Updated Oct 28, 2026Oct 28, 2026

• squidpy

  Public
  Spatial Single Cell Analysis in Python

  data-visualizationspatial-analysisimage-analysis+ 5

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

  Python

  •

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

  •128128 forks in scverse/squidpy•612612 stars in scverse/squidpy•8383 issues in scverse/squidpy•2626 pull requests in scverse/squidpy•Updated Oct 28, 2026Oct 28, 2026

• pytometry

  Public
  Flow & mass cytometry analytics.

  Python

  •

  Apache License 2.0

  •1515 forks in scverse/pytometry•6161 stars in scverse/pytometry•1313 issues in scverse/pytometry•55 pull requests in scverse/pytometry•Updated Oct 28, 2026Oct 28, 2026

• pertpy

  Public
  Single-cell perturbation analysis

  pythonbioinformaticscomputational-biology+ 10

  pythonbioinformaticscomputational-biologydrug-discoveryscrna-seqcrisprsingle-celldifferential-expressionperturbationanndata+ 3

  Python

  •

  MIT License

  •6969 forks in scverse/pertpy•354354 stars in scverse/pertpy•99 issues in scverse/pertpy•55 pull requests in scverse/pertpy•Updated Oct 28, 2026Oct 28, 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

  •2828 forks in scverse/mudata•134134 stars in scverse/mudata•1010 issues in scverse/mudata•22 pull requests in scverse/mudata•Updated Oct 28, 2026Oct 28, 2026

• ecosystem-packages

  Public
  Registry for scverse ecosystem packages

  Python

  •

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

  •9898 forks in scverse/ecosystem-packages•4242 stars in scverse/ecosystem-packages•66 issues in scverse/ecosystem-packages•2323 pull requests in scverse/ecosystem-packages•Updated Oct 28, 2026Oct 28, 2026

• spatialdata-io

  Public
  Python

  •

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

  •6565 forks in scverse/spatialdata-io•108108 stars in scverse/spatialdata-io•7070 issues in scverse/spatialdata-io•1717 pull requests in scverse/spatialdata-io•Updated Oct 28, 2026Oct 28, 2026

• scirpy

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

  airrscverse

  airrscverse

  Python

  •

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

  •5050 forks in scverse/scirpy•268268 stars in scverse/scirpy•3636 issues in scverse/scirpy•1111 pull requests in scverse/scirpy•Updated Oct 28, 2026Oct 28, 2026

• scverse.github.io

  Public
  scverse.org website

  SCSS

  •

  Mozilla Public License 2.0

  •1111 forks in scverse/scverse.github.io•44 stars in scverse/scverse.github.io•55 issues in scverse/scverse.github.io•22 pull requests in scverse/scverse.github.io•Updated Oct 28, 2026Oct 28, 2026

• scverse-misc

  Public
  Miscellaneous utility code used by scverse packages

  scverse

  scverse

  Python

  •

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

  •22 forks in scverse/scverse-misc•66 stars in scverse/scverse-misc•66 issues in scverse/scverse-misc•22 pull requests in scverse/scverse-misc•Updated Oct 28, 2026Oct 28, 2026

• scvi-tutorials

  Public
  Notebooks used in scvi-tools tutorials

  tutorialscvi-toolsscverse

  tutorialscvi-toolsscverse

  Jupyter Notebook

  •

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

  •3535 forks in scverse/scvi-tutorials•6565 stars in scverse/scvi-tutorials•00 issues in scverse/scvi-tutorials•55 pull requests in scverse/scvi-tutorials•Updated Oct 28, 2026Oct 28, 2026

• scvi-colab

  Public
  Lightweight helper to install scvi-tools in Google Colab

  googlecolabscvi-toolsscverse

  googlecolabscvi-toolsscverse

  Python

  •

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

  •11 fork in scverse/scvi-colab•22 stars in scverse/scvi-colab•00 issues in scverse/scvi-colab•00 pull requests in scverse/scvi-colab•Updated Oct 28, 2026Oct 28, 2026

• Muon.jl

  Public
  Muon for Julia

  juliamuonomics+ 5

  juliamuonomicssingle-cellmulti-omicsanndatamudatascverse

  Julia

  •

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

  •66 forks in scverse/Muon.jl•3030 stars in scverse/Muon.jl•11 issue in scverse/Muon.jl•00 pull requests in scverse/Muon.jl•Updated Oct 28, 2026Oct 28, 2026

• spatialdata

  Public
  An open and interoperable data framework for spatial omics data

  spatialspatial-analysisspatial-data+ 1

  spatialspatial-analysisspatial-datascverse

  Python

  •

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

  •106106 forks in scverse/spatialdata•404404 stars in scverse/spatialdata•315315 issues in scverse/spatialdata•4040 pull requests in scverse/spatialdata•Updated Oct 28, 2026Oct 28, 2026

• scvi-tools-site

  Public
  Website of scVI-Tools: Deep probabilistic analysis of single-cell and spatial omics data

  websitescvi-toolssinglecellgenomics+ 1

  websitescvi-toolssinglecellgenomicsscverse

  JavaScript

  •22 forks in scverse/scvi-tools-site•00 stars in scverse/scvi-tools-site•00 issues in scverse/scvi-tools-site•1111 pull requests in scverse/scvi-tools-site•Updated Oct 27, 2026Oct 27, 2026

• muon

  Public
  muon is a multimodal omics Python framework

  muonscrna-seqmulti-omics+ 8

  muonscrna-seqmulti-omicsmultimodal-datacite-seqscanpyscatac-seqanndatamultimodal-omics-analysismudata+ 1

  Python

  •

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

  •3636 forks in scverse/muon•279279 stars in scverse/muon•99 issues in scverse/muon•11 pull request in scverse/muon•Updated Oct 27, 2026Oct 27, 2026

• cookiecutter-scverse-presentation

  Public
  Introduction to our template

  00 forks in scverse/cookiecutter-scverse-presentation•22 stars in scverse/cookiecutter-scverse-presentation•00 issues in scverse/cookiecutter-scverse-presentation•00 pull requests in scverse/cookiecutter-scverse-presentation•Updated Oct 27, 2026Oct 27, 2026

• pandas-uuid

  Public
  Pandas ExtensionArray / ExtensionDType for UUID

  Python

  •

  Mozilla Public License 2.0

  •00 forks in scverse/pandas-uuid•33 stars in scverse/pandas-uuid•55 issues in scverse/pandas-uuid•00 pull requests in scverse/pandas-uuid•Updated Oct 27, 2026Oct 27, 2026

• scverse-tutorials

  Public
  Tutorials for learning scverse

  Python

  •

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

  •1818 forks in scverse/scverse-tutorials•2323 stars in scverse/scverse-tutorials•1212 issues in scverse/scverse-tutorials•77 pull requests in scverse/scverse-tutorials•Updated Oct 27, 2026Oct 27, 2026

• zulip-bots

  Public
  Repository for zulip bots for scverse.zulipchat.com

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

  •00 forks in scverse/zulip-bots•00 stars in scverse/zulip-bots•00 issues in scverse/zulip-bots•00 pull requests in scverse/zulip-bots•Updated Oct 27, 2026Oct 27, 2026