yjgeno/GenKI

R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.

Single-cell perturbation analysis

Modeling complex perturbations with CellFlow

Single-cell perturbation effects prediction benchmark

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.

Multiome GRN inference.

State is a machine learning model that predicts cellular perturbation response across diverse contexts

GeneCompass

Combined RNA and ATAC Footprint Training of Gene Regulatory Network