scverse/SnapATAC2

Deep probabilistic analysis of single-cell and spatial omics data

R toolkit for single cell genomics

Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports

10x Genomics Single Cell Analysis

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

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.

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

An R package for single-cell and spatial omics analysis, integration, interpretation, and visualization.

Single-cell perturbation analysis