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scanpy
Single-cell analysis in Python. Scales to >1M cells.scvi-tools
Deep probabilistic analysis of single-cell omics dataanndata
Annotated data.squidpy
Spatial Single Cell Analysis in Pythonspatialdata
An open and interoperable data framework for spatial omics datamuon
muon is a multimodal omics Python frameworkscirpy
A scanpy extension to analyse single-cell TCR and BCR data.scanpy-tutorials
Scanpy Tutorials.pertpy
Perturbation Analysis in the scverse ecosystem.scanpy_usage
Scanpy use cases.mudata
Multimodal Data (.h5mu) implementation for Pythoncookiecutter-scverse
Cookiecutter template for scverseanndataR
AnnData interoperability in Rnapari-spatialdata
Interactive visualization of spatial omics datascvi-tutorials
Notebooks used in scvi-tools tutorialsspatialdata-notebooks
spatialdata-io
spatialdata-plot
Static plotting for spatialdatasquidpy_notebooks
Tutorials for SquidpyMuon.jl
Muon for Juliascvi-tools-skeleton
Template repository for creating novel models with scvi-toolsecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)genomic-features
Genomic Features in Python from BioConductor's AnnotationHubanndata-tutorials
Use cases for anndata.muon-tutorials
Tutorials for multimodal omics data analysisscverse-tutorials
Tutorials for learning scversegovernance
Governance docs for scversepertpy-tutorials
simple-scvi
Example repo of using scvi-tools building blocks externally with simplified scVI implementationmulti-condition-comparisions
Functions for analyzing and visualizing multi-condition single-cell data (prototypes created at Cambridge hackathon)shadows
Shadow objects for AnnData and MuData (experimental)benchmark
Code for running benchmarkscookiecutter-scverse-instance
Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.scverse.github.io
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