scverse

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50 repositories

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
•82•440•61•5•Updated Nov 22, 2024Nov 22, 2024
anndata
Public
Annotated data.
data-science machine-learning bioinformatics transcriptomics scanpy anndata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•154•579•194•57•Updated Nov 22, 2024Nov 22, 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
•603•1.9k•513•73•Updated Nov 22, 2024Nov 22, 2024
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
•355•1.3k•48•13•Updated Nov 22, 2024Nov 22, 2024
spatialdata
Public
An open and interoperable data framework for spatial omics data
Python
•
BSD 3-Clause "New" or "Revised" License
•45•237•180•18•Updated Nov 22, 2024Nov 22, 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•46•8•7•Updated Nov 21, 2024Nov 21, 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
•22•153•15•4•Updated Nov 21, 2024Nov 21, 2024
pytometry
Public
Flow & mass cytometry analytics.
Python
•
Apache License 2.0
•9•42•12•0•Updated Nov 21, 2024Nov 21, 2024
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
Python
•
BSD 3-Clause "New" or "Revised" License
•34•221•39•5•Updated Nov 20, 2024Nov 20, 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•2•Updated Nov 18, 2024Nov 18, 2024
ecosystem-packages
Public
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Python
•
BSD 3-Clause "New" or "Revised" License
•40•19•6•5•Updated Nov 18, 2024Nov 18, 2024
scverse.github.io
Public
scverse.org website
SCSS
•6•1•17•2•Updated Nov 18, 2024Nov 18, 2024
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•9•70•19•1•Updated Nov 18, 2024Nov 18, 2024
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•0•1•0•Updated Nov 18, 2024Nov 18, 2024
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•116•188•16•2•Updated Nov 18, 2024Nov 18, 2024
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•13•13•13•5•Updated Nov 18, 2024Nov 18, 2024
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•14•37•62•8•Updated Nov 18, 2024Nov 18, 2024
plotting_api
Public
Experimenting with a simplified plotting API for scanpy/scirpy
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•1•2•2•Updated Nov 18, 2024Nov 18, 2024
napari-spatialdata
Public
Interactive visualization of spatial omics data
visualization spatial-analysis napari-plugin napari spatial-omics
Python
•
BSD 3-Clause "New" or "Revised" License
•17•41•51•6•Updated Nov 18, 2024Nov 18, 2024
genomic-features
Public
Genomic Features in Python from BioConductor's AnnotationHub
genomics python
Python
•
BSD 3-Clause "New" or "Revised" License
•5•19•19•7•Updated Nov 18, 2024Nov 18, 2024
anndataR
Public
AnnData interoperability in R
anndata h5ad
R
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Other
•11•60•22•12•Updated Nov 15, 2024Nov 15, 2024
pertpy-datasets
Public
Dataset preparation for pertpy
Jupyter Notebook
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MIT License
•1•1•1•0•Updated Nov 13, 2024Nov 13, 2024
spatialdata-basel-workshop-2024
Public
0•0•0•0•Updated Nov 13, 2024Nov 13, 2024
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•27•43•40•15•Updated Nov 12, 2024Nov 12, 2024
spatialdata-notebooks
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•19•38•6•7•Updated Nov 11, 2024Nov 11, 2024
squidpy_notebooks
Public
Tutorials for Squidpy
Jupyter Notebook
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MIT License
•18•30•6•2•Updated Nov 7, 2024Nov 7, 2024
integration-testing
Public
A repo for integration testing core packages against upstream core packages
MIT License
•0•0•0•0•Updated Nov 6, 2024Nov 6, 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•218•36•4•Updated Oct 30, 2024Oct 30, 2024
simple-scvi
Public
Simple scVI implementation
Python
•
BSD 3-Clause "New" or "Revised" License
•4•9•0•2•Updated Oct 28, 2024Oct 28, 2024
pertpy
Public
Perturbation Analysis in the scverse ecosystem.
single-cell perturbation scverse
Python
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MIT License
•21•141•35•1•Updated Oct 26, 2024Oct 26, 2024