title: HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  Source code in Julia and Python, and detailed documentation is available at https://github.com/gersteinlab/HiC-spector .
  
  
  BACKGROUND
  koonkiu.yan@gmail.com or mark@gersteinlab.org.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.|Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
authors.forename: Koon-Kiu
authors.initials: KK
authors.lastname: Yan
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
authors.forename: Galip Gürkan
authors.initials: GG
authors.lastname: Yardimci
authors.affiliation: Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.|Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
authors.forename: Chengfei
authors.initials: C
authors.lastname: Yan
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, USA.|Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
authors.forename: William S
authors.initials: WS
authors.lastname: Noble
authors.affiliation: Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.|Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.|Department of Computer Science, Yale University, New Haven, CT, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D019921:Biotinylation; D002875:Chromosomes / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D015723:Gene Library; D005821:Genetic Techniques; D016678:Genome; D006801:Humans; D015203:Reproducibility of Results
chemical_list: D004247:DNA