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

Dejun Lin, Justin Sanders, William Stafford Noble

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 assess 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.