title: GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.
abstract: BACKGROUND
  Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and the spatial organisation of chromatin is highly complex, interdependent and not completely understood. The development of experimental techniques to interrogate both the higher-order structure of chromatin and the interactions between regulatory elements has recently lead to important insights on how gene expression is controlled. The ability to gain these and future insights is critically dependent on computational tools for the analysis and visualisation of data produced by these techniques.
  
  
  CONCLUSIONS
  We have developed GenomicInteractions, a freely available R/Bioconductor package designed for processing, analysis and visualisation of data generated from various types of chromosome conformation capture experiments. The package allows the easy annotation and summarisation of large genome-wide datasets at both the level of individual interactions and sets of genomic features, and provides several different methods for interrogating and visualising this type of data. We demonstrate this package's utility by showing example analyses performed on interaction datasets generated using Hi-C and ChIA-PET.
authors.affiliation: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK. nathan.harmston@duke-nus.edu.sg.|Program in Cardiovascular and Metabolic Disease, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore. nathan.harmston@duke-nus.edu.sg.
authors.forename: Nathan
authors.initials: N
authors.lastname: Harmston
authors.affiliation: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK. liz.ing-simmons12@imperial.ac.uk.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Ing-Simmons
authors.affiliation: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK. m.perry13@imperial.ac.uk.
authors.forename: Malcolm
authors.initials: M
authors.lastname: Perry
authors.affiliation: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK. abaresic@imperial.ac.uk.
authors.forename: Anja
authors.initials: A
authors.lastname: Barešić
authors.affiliation: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, W12 0NN, UK. b.lenhard@imperial.ac.uk.
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D003196:Computer Graphics; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D006801:Humans; D020014:K562 Cells; D051379:Mice; D058977:Molecular Sequence Annotation; D012984:Software; D060168:Thymocytes / Q000378:metabolism
chemical_list: D002843:Chromatin