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

    1 month ago - By Oxford Journals

    AbstractMotivationHi-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.ResultsWe introduce a Python implementation of HiCRep and demonstrate...
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