scverse

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52 repositories

anndata
Public
Annotated data.
data-science machine-learning bioinformatics transcriptomics scanpy anndata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•157•598•197•52•Updated Feb 3, 2025Feb 3, 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
•
BSD 3-Clause "New" or "Revised" License
•374•1.3k•45•14•Updated Feb 3, 2025Feb 3, 2025
spatialdata
Public
An open and interoperable data framework for spatial omics data
Python
•
BSD 3-Clause "New" or "Revised" License
•47•249•187•6•Updated Feb 2, 2025Feb 2, 2025
spatialdata-notebooks
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•19•40•5•0•Updated Feb 1, 2025Feb 1, 2025
ecosystem-packages
Public
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Python
•
BSD 3-Clause "New" or "Revised" License
•40•19•6•6•Updated Feb 1, 2025Feb 1, 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
•
BSD 3-Clause "New" or "Revised" License
•88•459•76•6•Updated Jan 30, 2025Jan 30, 2025
pertpy
Public
Perturbation Analysis in the scverse ecosystem.
single-cell perturbation scverse
Python
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MIT License
•25•149•34•3•Updated Jan 30, 2025Jan 30, 2025
muon
Public
muon is a multimodal omics Python framework
muon scrna-seq multi-omics multimodal-data cite-seq scanpy scatac-seq anndata multimodal-omics-analysis mudata
Python
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BSD 3-Clause "New" or "Revised" License
•30•224•38•5•Updated Jan 30, 2025Jan 30, 2025
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
Python
•
BSD 3-Clause "New" or "Revised" License
•36•224•40•5•Updated Jan 30, 2025Jan 30, 2025
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•32•47•45•11•Updated Jan 28, 2025Jan 28, 2025
scverse.github.io
Public
scverse.org website
SCSS
•6•1•16•2•Updated Jan 28, 2025Jan 28, 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
•
MIT License
•25•168•15•3•Updated Jan 28, 2025Jan 28, 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
•27•51•8•6•Updated Jan 28, 2025Jan 28, 2025
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•0•2•3•1•Updated Jan 28, 2025Jan 28, 2025
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•15•43•67•3•Updated Jan 28, 2025Jan 28, 2025
scanpy
Public
Single-cell analysis in Python. Scales to >1M cells.
data-science machine-learning bioinformatics transcriptomics visualize-data scanpy anndata scverse python
Python
•
BSD 3-Clause "New" or "Revised" License
•612•2k•490•67•Updated Jan 28, 2025Jan 28, 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
•
BSD 3-Clause "New" or "Revised" License
•2•1•0•2•Updated Jan 27, 2025Jan 27, 2025
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•10•72•21•1•Updated Jan 27, 2025Jan 27, 2025
governance
Public
Governance docs for scverse
governance scverse
BSD 3-Clause "New" or "Revised" License
•0•7•19•2•Updated Jan 27, 2025Jan 27, 2025
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•0•1•0•Updated Jan 27, 2025Jan 27, 2025
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•13•14•13•5•Updated Jan 27, 2025Jan 27, 2025
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•118•196•15•1•Updated Jan 27, 2025Jan 27, 2025
pytometry
Public
Flow & mass cytometry analytics.
Python
•
Apache License 2.0
•8•43•11•1•Updated Jan 27, 2025Jan 27, 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
•6•20•19•8•Updated Jan 27, 2025Jan 27, 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
•17•47•53•1•Updated Jan 27, 2025Jan 27, 2025
formulaic-contrasts
Public
Build contrasts for models defined with formulaic
Python
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BSD 3-Clause "New" or "Revised" License
•1•11•2•1•Updated Jan 27, 2025Jan 27, 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•1•3•2•Updated Jan 27, 2025Jan 27, 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•1•2•0•Updated Jan 26, 2025Jan 26, 2025
anndataR
Public
AnnData interoperability in R
anndata h5ad
R
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Other
•11•68•18•4•Updated Jan 24, 2025Jan 24, 2025
mudata
Public
Multimodal Data (.h5mu) implementation for Python
genomics muon data-analysis multi-omics anndata multimodal-omics-analysis mudata scverse
Python
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BSD 3-Clause "New" or "Revised" License
•19•83•17•4•Updated Jan 20, 2025Jan 20, 2025