HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data.

ABSTRACT: Eukaryotic genomes are organized in a three-dimensional spatial structure. In this regard, the development of chromosome conformation capture methods has enabled studies of chromosome organization on a genomic scale. Hi-C, the high-throughput chromosome conformation capture method, can reveal a population-averaged, hierarchical chromatin structure. The typical Hi-C analysis uses a two-dimensional (2D) contact matrix that indicates contact frequencies between all possible genomic position pairs. Oftentimes, however, such a 2D matrix is not amenable to handling quantitative comparisons, visualizations and integrations across multiple datasets. Although several one-dimensional (1D) metrics have been proposed to depict structural information in Hi-C data, their effectiveness is still underappr

SUBMITTER: Wang J 

PROVIDER: S-EPMC8769930 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature