@article {Yan088922, author = {Koon-Kiu Yan and Galip Gu{\"u}rkan Yardimci and William S. Noble and Mark Gerstein}, title = {HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps}, elocation-id = {088922}, year = {2016}, doi = {10.1101/088922}, publisher = {Cold Spring Harbor Laboratory}, 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 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}, URL = {https://www.biorxiv.org/content/early/2016/11/21/088922}, eprint = {https://www.biorxiv.org/content/early/2016/11/21/088922.full.pdf}, journal = {bioRxiv} }