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

<p>This repository accompanies the manuscript &quot;<strong>Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations</strong>&quot;, to appear in Nat. Methods (2022), see also&nbsp;https://www.biorxiv.org/content/10.1101/2021.08.22.457288v1.</p> <p>It&nbsp;contains the preprocessed input data files (Hi-C, laminB1 DamID, 3D&nbsp;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).</p> <p>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 &quot;hss&quot; file. Documentation and a simple demo/tutorial on how IGM can be run is given on the Alber lab Github @&nbsp;https://github.com/alberlab/igm.</p> <p>All files can be read in using the&nbsp;<em>h5py</em> and <em>alabtools</em> (available @https://github.com/alberlab/alabtools) Python packages. More detailed information is provided in the manuscript and associated Supplementary Information file.&nbsp;&nbsp;</p> <p>For any inquiry/suggestions/doubts please reach out to Lorenzo Boninsegna (bonimba@g.ucla.edu) or Dr. Frank Alber (falber@g.ucla.edu).</p> <p>&nbsp;</p>