PT  - JOURNAL ARTICLE
AU  - Koon-Kiu Yan
AU  - Galip Guürkan Yardimci
AU  - William S. Noble
AU  - Mark Gerstein
TI  - HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps
AID  - 10.1101/088922
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 088922
4099  - http://biorxiv.org/content/early/2016/11/21/088922.short
4100  - http://biorxiv.org/content/early/2016/11/21/088922.full
AB  - 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 Source code in Julia and the documentation of HiC-spector can be freely obtained at https://github.com/gersteinlab/HiC_spectorContact pi{at}gersteinlab.org