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bioRxiv · 10.1101/2020.10.27.357756

HiCRep.py: Fast comparison of Hi-C contact matrices in Python

Lin, D.·Sanders, J.·Noble, W. S.
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Abstract

Hi-C is the most widely used assay for investigating genome-wide 3D organization of chromatin. When working with Hi-C data, it is often useful to calculate the similarity between contact matrices in order to asses experimental reproducibility or to quantify relationships among Hi-C data from related samples. The HiCRep algorithm has been widely adopted for this task, but the existing R implementation suffers from run time limitations on high resolution Hi-C data or on large single-cell Hi-C datasets. We introduce a Python implementation of HiCRep and demonstrate that it is much faster than the existing R implementation. Furthermore, we give examples of HiCReps ability to accurately distinguish replicates from non-replicates and to reveal cell type structure among collections of Hi-C data. HiCRep.py and its documentation are available with a GPL license at https://github.com/Noble-Lab/hicrep. The software may be installed automatically using the pip package installer.

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Lin, D., Sanders, J., Noble, W. S.. 2020-10-28. HiCRep.py: Fast comparison of Hi-C contact matrices in Python. https://doi.org/10.1101/2020.10.27.357756

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