EngreitzLab/scE2G

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

Multiome GRN inference.

Accurate and fast cell marker gene identification with COSG

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

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.

Accurate and fast cell marker gene identification with COSG

Single-cell epigenomics analysis tools

SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

Metacells - Single-cell RNA Sequencing Analysis