scverse repositories

97 repositories

anndataR
Public
AnnData interoperability in R
interoperability anndata h5ad
interoperability anndata h5ad
R
•
Other
•22•196•40•12•Updated Sep 13, 2026Sep 13, 2026
rapids-singlecell
Public
rapids-singlecell: GPU-accelerated framework for scRNA analysis
bioinformatics gpu single-cell
bioinformatics gpu single-cell anndata scverse
Python
•
MIT License
•52•394•14•9•Updated Sep 13, 2026Sep 13, 2026
scverse-doc
Public
scverse doc theme & utilities
Python
•
Mozilla Public License 2.0
•0•2•3•1•Updated Sep 13, 2026Sep 13, 2026
liana
Public
LIANA+: an all-in-one framework for cell-cell communication
python spatial single-cell
python spatial single-cell single-cell-rna-seq ligand-receptor cell-cell-communication spatialomics
Python
•
BSD 3-Clause "New" or "Revised" License
•37•315•10•1•Updated Sep 13, 2026Sep 13, 2026
liana-tutorials
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Sep 13, 2026Sep 13, 2026
SnapATAC2
Public
Single-cell epigenomics analysis tools
single-cell-genomics scverse
single-cell-genomics scverse
Python
•
MIT License
•43•323•68•3•Updated Sep 12, 2026Sep 12, 2026
acumen
Public
Python
•
MIT License
•1•8•1•1•Updated Sep 12, 2026Sep 12, 2026
spatialdata
Public
An open and interoperable data framework for spatial omics data
spatial spatial-analysis spatial-data
spatial spatial-analysis spatial-data scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•94•392•308•19•Updated Sep 11, 2026Sep 11, 2026
decoupler
Public
Python package to perform enrichment analysis from omics data.
python data-science bioinformatics
python data-science bioinformatics enrichment numba transcriptomics single-cell enrichment-analysis spatial-transcriptomics scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•38•293•3•2•Updated Sep 11, 2026Sep 11, 2026
scverse.github.io
Public
scverse.org website
SCSS
•
Mozilla Public License 2.0
•11•4•6•4•Updated Sep 11, 2026Sep 11, 2026
scverse-misc
Public
Miscellaneous utility code used by scverse packages
scverse
scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•2•5•7•3•Updated Sep 11, 2026Sep 11, 2026
scanpy
Public
Single-cell analysis in Python. Scales to >100M cells.
python data-science machine-learning
python data-science machine-learning bioinformatics transcriptomics visualize-data scanpy anndata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•777•2.6k•446•94•Updated Sep 11, 2026Sep 11, 2026
2026_09_workshop_physalia
Public
https://www.physalia-courses.org/courses-workshops/scverse/
Shell
•0•0•0•0•Updated Sep 11, 2026Sep 11, 2026
gget
Public
🧬 gget enables efficient querying of genomic reference databases
rna-seq genomics reference
rna-seq genomics reference databases ensembl proteomics blast transcriptomics uniprot ncbi
Python
•
BSD 2-Clause "Simplified" License
•95•1.2k•25•18•Updated Sep 11, 2026Sep 11, 2026
squidpy
Public
Spatial Single Cell Analysis in Python
data-visualization spatial-analysis image-analysis
data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•121•598•78•25•Updated Sep 10, 2026Sep 10, 2026
anndata
Public
Annotated data.
data-science machine-learning bioinformatics
data-science machine-learning bioinformatics transcriptomics scanpy anndata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•208•771•187•84•Updated Sep 10, 2026Sep 10, 2026
scvi-tools
Public
Deep probabilistic analysis of single-cell and spatial omics data
deep-learning scrna-seq variational-autoencoder
deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•473•1.7k•12•12•Updated Sep 10, 2026Sep 10, 2026
scvi-tutorials
Public
Notebooks used in scvi-tools tutorials
tutorial scvi-tools scverse
tutorial scvi-tools scverse
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•35•65•0•4•Updated Sep 10, 2026Sep 10, 2026
scvi-colab
Public
Lightweight helper to install scvi-tools in Google Colab
googlecolab scvi-tools scverse
googlecolab scvi-tools scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•1•2•0•0•Updated Sep 10, 2026Sep 10, 2026
benchmark
Public
Code for running benchmarks
Rust
•
GNU General Public License v3.0
•0•4•7•1•Updated Sep 10, 2026Sep 10, 2026
pertpy
Public
Single-cell perturbation analysis
python bioinformatics computational-biology
python bioinformatics computational-biology drug-discovery scrna-seq crispr single-cell differential-expression perturbation anndata
Python
•
MIT License
•66•342•9•4•Updated Sep 10, 2026Sep 10, 2026
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
airr scverse
airr scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•49•265•35•10•Updated Sep 10, 2026Sep 10, 2026
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•18•22•12•7•Updated Sep 9, 2026Sep 9, 2026
spatialdata-integration-testing
Public
Integration testing for the SpatialData framework
Python
•
BSD 3-Clause "New" or "Revised" License
•1•2•0•0•Updated Sep 9, 2026Sep 9, 2026
spatialdata-tutorials
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•26•67•8•0•Updated Sep 9, 2026Sep 9, 2026
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•63•102•69•9•Updated Sep 9, 2026Sep 9, 2026
muon
Public
muon is a multimodal omics Python framework
muon scrna-seq multi-omics
muon scrna-seq multi-omics multimodal-data cite-seq scanpy scatac-seq anndata multimodal-omics-analysis mudata
Python
•
BSD 3-Clause "New" or "Revised" License
•37•279•10•1•Updated Sep 9, 2026Sep 9, 2026
mudata
Public
Multimodal Data (.h5mu) implementation for Python
genomics muon data-analysis
genomics muon data-analysis multi-omics anndata multimodal-omics-analysis mudata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•23•134•8•0•Updated Sep 8, 2026Sep 8, 2026
annbatch
Public
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Python
•
MIT License
•6•68•24•11•Updated Sep 8, 2026Sep 8, 2026
napari-spatialdata
Public
Interactive visualization of spatial omics data
visualization spatial-analysis napari-plugin
visualization spatial-analysis napari-plugin napari spatial-omics
Python
•
BSD 3-Clause "New" or "Revised" License
•25•89•68•4•Updated Sep 8, 2026Sep 8, 2026

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97 repositories

anndataR

rapids-singlecell

scverse-doc

liana

liana-tutorials

SnapATAC2

acumen

spatialdata

decoupler

scverse.github.io

scverse-misc

scanpy

2026_09_workshop_physalia

gget

squidpy

anndata

scvi-tools

scvi-tutorials

scvi-colab

benchmark

pertpy

scirpy

scverse-tutorials

spatialdata-integration-testing

spatialdata-tutorials

spatialdata-io

muon

mudata

annbatch

napari-spatialdata

Repositories list

97 repositories