scverse

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60 repositories

ecosystem-packages
Public
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Python
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BSD 3-Clause "New" or "Revised" License
•52•24•7•9•Updated Jul 1, 2025Jul 1, 2025
scvi-tools
Public
Deep probabilistic analysis of single-cell and spatial omics data
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
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BSD 3-Clause "New" or "Revised" License
•398•1.4k•39•9•Updated Jul 1, 2025Jul 1, 2025
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 template.
Python
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BSD 3-Clause "New" or "Revised" License
•4•4•0•3•Updated Jun 30, 2025Jun 30, 2025
plotting_api
Public
Experimenting with a simplified plotting API for scanpy/scirpy
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•2•3•2•Updated Jun 30, 2025Jun 30, 2025
cookiecutter-scverse-presentation
Public
Introduction to our template
0•1•0•1•Updated Jun 30, 2025Jun 30, 2025
zulip-bots
Public
Repository for zulip bots for scverse.zulipchat.com
BSD 3-Clause "New" or "Revised" License
•0•0•0•1•Updated Jun 30, 2025Jun 30, 2025
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•17•61•91•14•Updated Jun 30, 2025Jun 30, 2025
spatialdata-notebooks
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•21•53•6•1•Updated Jun 30, 2025Jun 30, 2025
genomic-features
Public
Genomic Features in Python from BioConductor's AnnotationHub
genomics python
Python
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BSD 3-Clause "New" or "Revised" License
•5•22•19•8•Updated Jun 30, 2025Jun 30, 2025
spatialdata
Public
An open and interoperable data framework for spatial omics data
Python
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BSD 3-Clause "New" or "Revised" License
•63•289•211•18•Updated Jun 30, 2025Jun 30, 2025
squidpy
Public
Spatial Single Cell Analysis in Python
data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy
Python
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BSD 3-Clause "New" or "Revised" License
•96•493•78•11•Updated Jun 30, 2025Jun 30, 2025
spatialdata-io
Public
Python
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BSD 3-Clause "New" or "Revised" License
•36•63•47•14•Updated Jun 30, 2025Jun 30, 2025
scverse-tutorials
Public
Tutorials for learning scverse
Python
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BSD 3-Clause "New" or "Revised" License
•13•16•11•7•Updated Jun 30, 2025Jun 30, 2025
decoupler
Public
Python package to perform enrichment analysis from omics data.
python data-science bioinformatics enrichment numba transcriptomics single-cell enrichment-analysis spatial-transcriptomics
Python
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BSD 3-Clause "New" or "Revised" License
•31•210•3•1•Updated Jun 30, 2025Jun 30, 2025
pertpy
Public
Perturbation Analysis in the scverse ecosystem.
single-cell perturbation scverse
Python
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MIT License
•32•183•31•5•Updated Jun 30, 2025Jun 30, 2025
scvi-tutorials
Public
Notebooks used in scvi-tools tutorials
scvi-tools scverse tutorial
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•28•54•6•5•Updated Jun 30, 2025Jun 30, 2025
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
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BSD 3-Clause "New" or "Revised" License
•12•78•22•2•Updated Jun 30, 2025Jun 30, 2025
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•118•217•15•4•Updated Jun 30, 2025Jun 30, 2025
scvi-colab
Public
Lightweight helper to install scvi-tools in Google Colab
Python
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BSD 3-Clause "New" or "Revised" License
•1•2•1•1•Updated Jun 30, 2025Jun 30, 2025
scverse.github.io
Public
scverse.org website
HTML
•7•3•17•1•Updated Jun 30, 2025Jun 30, 2025
pytometry
Public
Flow & mass cytometry analytics.
Python
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Apache License 2.0
•10•52•12•2•Updated Jun 30, 2025Jun 30, 2025
scanpy
Public
Single-cell analysis in Python. Scales to >100M cells.
python data-science machine-learning bioinformatics transcriptomics visualize-data scanpy anndata scverse
Python
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BSD 3-Clause "New" or "Revised" License
•647•2.1k•481•73•Updated Jun 30, 2025Jun 30, 2025
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
Python
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BSD 3-Clause "New" or "Revised" License
•38•234•39•4•Updated Jun 30, 2025Jun 30, 2025
rapids_singlecell
Public
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
bioinformatics gpu single-cell anndata scverse
Python
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MIT License
•26•216•16•5•Updated Jun 30, 2025Jun 30, 2025
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
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Apache License 2.0
•0•1•1•1•Updated Jun 30, 2025Jun 30, 2025
napari-spatialdata
Public
Interactive visualization of spatial omics data
visualization spatial-analysis napari-plugin napari spatial-omics
Python
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BSD 3-Clause "New" or "Revised" License
•19•61•61•4•Updated Jun 30, 2025Jun 30, 2025
anndata
Public
Annotated data.
data-science machine-learning bioinformatics transcriptomics scanpy anndata scverse
Python
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BSD 3-Clause "New" or "Revised" License
•166•632•194•56•Updated Jun 30, 2025Jun 30, 2025
fast-array-utils
Public
Fast array utilities
Python
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Mozilla Public License 2.0
•0•9•14•3•Updated Jun 30, 2025Jun 30, 2025
formulaic-contrasts
Public
Build contrasts for models defined with formulaic
Python
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BSD 3-Clause "New" or "Revised" License
•2•13•2•3•Updated Jun 30, 2025Jun 30, 2025
anndata-plot
Public
Python
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MIT License
•3•9•1•4•Updated Jun 30, 2025Jun 30, 2025