IGM Population of HFF structures using Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE data

This repository accompanies the manuscript "Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations", to appear in Nat. Methods (2022), see also https://www.biorxiv.org/content/10.1101/2021.08.22.457288v1.

It contains the preprocessed input data files (Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE) for the HFF fibroblast cell line to be used in the Integrative Genome Modeling platform (IGM) developed in the Alber lab at UCLA (https://github.com/alberlab/igm).

Also, we provide the configuration file to run IGM with those datasets, as we did in generating the HDSF population discussed in the accompanying manuscript. Such population is also provided as an "hss" file. Documentation and a simple demo/tutorial on how IGM can be run is given on the Alber lab Github @ https://github.com/alberlab/igm.

All files can be read in using the h5py and alabtools (available @https://github.com/alberlab/alabtools) Python packages. More detailed information is provided in the manuscript and associated Supplementary Information file.  

For any inquiry/suggestions/doubts please reach out to Lorenzo Boninsegna ([e-mail]) or Dr. Frank Alber ([e-mail]).