scverse/pertpy

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

CellRank: dynamics from multi-view single-cell data

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

Cell2Sentence: Teaching Large Language Models the Language of Biology

rapids-singlecell: GPU-accelerated framework for scRNA analysis

Spatial Single Cell Analysis in Python

Deep probabilistic analysis of single-cell and spatial omics data

Single-cell epigenomics analysis tools

LIANA+: an all-in-one framework for cell-cell communication