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

Koon-Kiu Yan, Galip Guürkan Yardimci, William S. Noble, Mark Gerstein
doi: https://doi.org/10.1101/088922
Koon-Kiu Yan
1Program in Computational Biology and Bioinformatics, University of Washington, Seattle
2Department of Molecular Biophysics and Biochemistry, University of Washington, Seattle
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Galip Guürkan Yardimci
4Department of Genome Sciences, University of Washington, Seattle
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William S. Noble
4Department of Genome Sciences, University of Washington, Seattle
5Department of Computer Science and Engineering, University of Washington, Seattle
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Mark Gerstein
1Program in Computational Biology and Bioinformatics, University of Washington, Seattle
2Department of Molecular Biophysics and Biochemistry, University of Washington, Seattle
3Department of Computer Science, Yale University, University of Washington, Seattle
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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_spector

Contact pi{at}gersteinlab.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 21, 2016.
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HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps
Koon-Kiu Yan, Galip Guürkan Yardimci, William S. Noble, Mark Gerstein
bioRxiv 088922; doi: https://doi.org/10.1101/088922
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HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps
Koon-Kiu Yan, Galip Guürkan Yardimci, William S. Noble, Mark Gerstein
bioRxiv 088922; doi: https://doi.org/10.1101/088922

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