scverse

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51 repositories

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
•366•1.3k•42•9•Updated Dec 25, 2024Dec 25, 2024
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
•23•158•15•3•Updated Dec 23, 2024Dec 23, 2024
spatialdata-notebooks
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•19•39•6•5•Updated Dec 23, 2024Dec 23, 2024
spatialdata-plot
Public
Static plotting for spatialdata
Python
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BSD 3-Clause "New" or "Revised" License
•14•38•65•8•Updated Dec 23, 2024Dec 23, 2024
simple-scvi
Public
Simple scVI implementation
Python
•
BSD 3-Clause "New" or "Revised" License
•4•9•0•2•Updated Dec 23, 2024Dec 23, 2024
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
Python
•
BSD 3-Clause "New" or "Revised" License
•35•222•39•6•Updated Dec 23, 2024Dec 23, 2024
pytometry
Public
Flow & mass cytometry analytics.
Python
•
Apache License 2.0
•9•42•11•1•Updated Dec 23, 2024Dec 23, 2024
cookiecutter-scverse-presentation
Public
Introduction to our template
0•0•0•1•Updated Dec 23, 2024Dec 23, 2024
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
•84•448•70•6•Updated Dec 23, 2024Dec 23, 2024
spatialdata-io
Public
Python
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BSD 3-Clause "New" or "Revised" License
•29•45•45•13•Updated Dec 23, 2024Dec 23, 2024
spatialdata
Public
An open and interoperable data framework for spatial omics data
Python
•
BSD 3-Clause "New" or "Revised" License
•47•245•180•15•Updated Dec 23, 2024Dec 23, 2024
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
•25•47•8•7•Updated Dec 23, 2024Dec 23, 2024
scverse-tutorials
Public
Tutorials for learning scverse
Python
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BSD 3-Clause "New" or "Revised" License
•13•14•13•6•Updated Dec 23, 2024Dec 23, 2024
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
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Apache License 2.0
•0•0•1•1•Updated Dec 23, 2024Dec 23, 2024
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•3•Updated Dec 23, 2024Dec 23, 2024
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•117•192•16•3•Updated Dec 23, 2024Dec 23, 2024
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
•608•2k•507•76•Updated Dec 23, 2024Dec 23, 2024
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
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BSD 3-Clause "New" or "Revised" License
•10•71•20•2•Updated Dec 23, 2024Dec 23, 2024
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 Dec 23, 2024Dec 23, 2024
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•42•52•1•Updated Dec 23, 2024Dec 23, 2024
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 Dec 23, 2024Dec 23, 2024
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•19•19•8•Updated Dec 23, 2024Dec 23, 2024
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
•40•19•6•7•Updated Dec 23, 2024Dec 23, 2024
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
•156•588•193•55•Updated Dec 23, 2024Dec 23, 2024
scverse.github.io
Public
scverse.org website
SCSS
•6•1•17•2•Updated Dec 20, 2024Dec 20, 2024
anndataR
Public
AnnData interoperability in R
anndata h5ad
R
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Other
•11•64•21•5•Updated Dec 19, 2024Dec 19, 2024
rapids_singlecell-notebooks
Public
Jupyter Notebook
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MIT License
•1•3•0•0•Updated Dec 19, 2024Dec 19, 2024
spatialdata-basel-workshop-2024
Public
TeX
•1•0•0•0•Updated Dec 17, 2024Dec 17, 2024
pertpy-datasets
Public
Datasets provided through pertpy
Jupyter Notebook
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MIT License
•1•1•1•0•Updated Dec 17, 2024Dec 17, 2024
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
•31•222•38•5•Updated Dec 17, 2024Dec 17, 2024