theislab/scvelo

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

CellRank: dynamics from multi-view single-cell data

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

R toolkit for single cell genomics

Deep probabilistic analysis of single-cell and spatial omics data

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

10x Genomics Single Cell Analysis

A list of scRNA-seq analysis tools

Spatial Single Cell Analysis in Python