scverse

scanpy

Single-cell analysis in Python. Scales to >100M cells.

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

anndata

Annotated data.

squidpy

Spatial Single Cell Analysis in Python

spatialdata

An open and interoperable data framework for spatial omics data

rapids_singlecell

rapids_singlecell: GPU-accelerated framework for scRNA analysis

scirpy

A scanpy extension to analyse single-cell TCR and BCR data.

scanpy-tutorials

Scanpy Tutorials.

pertpy

Single-cell perturbation analysis

anndataR

AnnData interoperability in R

mudata

Multimodal Data (.h5mu) implementation for Python

cookiecutter-scverse

Cookiecutter template for scverse

spatialdata-io

napari-spatialdata

Interactive visualization of spatial omics data

spatialdata-plot

Static plotting for spatialdata

spatialdata-notebooks

scvi-tutorials

Notebooks used in scvi-tools tutorials

pytometry

Flow & mass cytometry analytics.

squidpy_notebooks

Tutorials for Squidpy

ecosystem-packages

Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

genomic-features

Genomic Features in Python from BioConductor's AnnotationHub

scverse-tutorials

Tutorials for learning scverse

anndata-tutorials

Use cases for anndata.

simple-scvi

Simple scVI implementation

pertpy-tutorials

shadows

Shadow objects for AnnData and MuData (experimental)

cookiecutter-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

scverse.org website

plotting_api

Experimenting with a simplified plotting API for scanpy/scirpy

prelude-runner

Jupyter notebook runner that executes preludes before each cell