anndata

totalVIscverse/scvi-tools

A Python library for deep probabilistic modeling and analysis of single-cell and spatial omics data.

Squidpyscverse/squidpy

A scalable Python toolkit for analyzing and visualizing spatial molecular data from tissue sections.

CellTypistTeichlab/celltypist

An automated cell type annotation tool for single-cell RNA-seq data using logistic regression classifiers.

scIB (Single-cell Integration Benchmarks)theislab/scib

A Python package for benchmarking and evaluating single-cell genomics data integration methods.