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bioRxiv · 10.1101/088922

HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps

Yan, K.-K.·Yardımcı, G. G.·Noble, W. S.·Gerstein, M.
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Abstract

SummaryGenome-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.\n\nAvailabilitySource code in Julia and the documentation of HiC-spector can be freely obtained at https://github.com/gersteinlab/HiC_spector\n\nContactpi@gersteinlab.org

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Yan, K.-K., Yardımcı, G. G., Noble, W. S., Gerstein, M.. 2016-11-21. HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps. https://doi.org/10.1101/088922

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