scverse/anndata-tutorials

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Created almost 7 years ago
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scverse/anndata-tutorials

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Use cases for anndata.

scanpy

Single-cell analysis in Python. Scales to >1M cells.

scvi-tools

Deep probabilistic analysis of single-cell omics data

anndata

Annotated data.

squidpy

Spatial Single Cell Analysis in Python

spatialdata

An open and interoperable data framework for spatial omics data

muon

muon is a multimodal omics Python framework

scirpy

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

scanpy-tutorials

Scanpy Tutorials.

Jupyter Notebook

pertpy

Perturbation Analysis in the scverse ecosystem.

scanpy_usage

Scanpy use cases.

mudata

Multimodal Data (.h5mu) implementation for Python

cookiecutter-scverse

Cookiecutter template for scverse

anndataR

AnnData interoperability in R

pytometry

Flow & mass cytometry analytics.

napari-spatialdata

Interactive visualization of spatial omics data

scvi-tutorials

Notebooks used in scvi-tools tutorials

Jupyter Notebook

spatialdata-notebooks

Jupyter Notebook

spatialdata-io

spatialdata-plot

Static plotting for spatialdata

squidpy_notebooks

Tutorials for Squidpy

Jupyter Notebook

Muon.jl

scvi-tools-skeleton

Template repository for creating novel models with scvi-tools

ecosystem-packages

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

genomic-features

Genomic Features in Python from BioConductor's AnnotationHub

muon-tutorials

Tutorials for multimodal omics data analysis

Jupyter Notebook

scverse-tutorials

Tutorials for learning scverse

governance

Governance docs for scverse

pertpy-tutorials

Jupyter Notebook

simple-scvi

Example repo of using scvi-tools building blocks externally with simplified scVI implementation

multi-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 benchmarks

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