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

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 and consume much less memory than the existing R implementation. Furthermore, we give examples of HiCRep's ability to accurately distinguish replicates from non-replicates and to reveal cell type structure am

SUBMITTER: Lin D 

PROVIDER: S-EPMC8479650 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature