Snakemake pipeline for running TOBIAS analysis

Integrated Genome Modeling

ROSE: RANK ORDERING OF SUPER-ENHANCERS

New Version tools for lab utilities

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

HiCARN: Resolution Enhancement of Hi-C Data Using Cascading Residual Networks

Population of Genome Structures modeling tools package

nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder

A modular Hi-C mapping pipeline

Gene regulatory network inference for RNA velocity and pseudotime data

Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""

PyTorch Tutorial for Deep Learning Researchers

"Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks" by Peter K. Koo and Sean R. Eddy