Durenlab/LINGER

Multiome GRN inference.

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.

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

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

Metacells - Single-cell RNA Sequencing Analysis

inferring regulatory cellular dynamics

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

Unsupervised Deep Disentangled Representation of Single-Cell Omics

Gene Set Enrichment Analysis in Python