This is the code for Lee et al. bioRxiv 2018 https://www.biorxiv.org/content/early/2018/12/26/503235
Requirements:
Python 2.7/3.4+ libhdf5 and Python packages numpy, scipy, pandas, h5py. We highly recommend using the conda package manager to install scientific packages like these. To get it, you can either install the full Anaconda Python distribution or just the standalone conda package manager.
Cooler: Please see https://github.com/mirnylab/cooler for installation and details
hicrep: Please see https://bioconductor.org/packages/release/bioc/html/hicrep.html for installation and details
Visualization: We use Higlass (https://github.com/higlass/higlass) for visualizing contact matrix map