aristoteleo/dynamo-release

CellRank: dynamics from multi-view single-cell data

RNA Velocity generalized through dynamical modeling

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.

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

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

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

R toolkit for single cell genomics