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

Dejun Lin | Zendy; Justin J. Sanders | Zendy; William Stafford Noble | Zendy

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

Author(s) -

Dejun Lin,

Justin J. Sanders,

William Stafford Noble

Publication year - 2021

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btab097

Subject(s) - python (programming language) , computer science , mit license , documentation , mac os , software , data mining , programming language

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.

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