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

• DOI: 10.1093/bioinformatics/btx152
• Publication Date: 2017-03-22T00:55:07Z
• Authors: Koon-Kiu Yan; Galip Gürkan Yard...; Chengfei Yan; William S Noble; Mark Gerstein
• Keywords: Matrix (chemical analysis)

Genome-wide proximity ligation based assays like Hi-C have opened a window to the 3D organization of genome. In so doing, they present data structures that are different from conventional 1D signal tracks. To exploit 2D nature contact maps, matrix techniques spectral analysis particularly useful. Here, we HiC-spector, collection matrix-related functions for analyzing maps. particular, introduce novel reproducibility metric quantifying similarity between maps on decomposition. The successfully separates mapped coming biological replicates, pseudo-replicates and cell types.Source code in Julia Python, detailed documentation is available at https://github.com/gersteinlab/HiC-spector [e-mail] or [e-mail] Bioinformatics online.