HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.

ABSTRACT:

Summary

Genome-wide proximity ligation based assays like Hi-C have opened a window to the 3D organization of the genome. In so doing, they present data structures that are different from conventional 1D signal tracks. To exploit the 2D nature of Hi-C contact maps, matrix techniques like spectral analysis are particularly useful. Here, we present HiC-spector, a collection of matrix-related functions for analyzing Hi-C contact maps. In particular, we introduce a novel reproducibility metric for quantifying the similarity between contact maps based on spectral decomposition. The metric successfully separates contact maps mapped from Hi-C data coming from biological replicates, pseudo-replicates and different cell types.

Availability and implementation

Source code in Julia and P

SUBMITTER: Yan KK 

PROVIDER: S-EPMC5870694 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature