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GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

Harmston, Nathan; Ing-Simmons, Elizabeth; Perry, Malcolm; Barešić, Anja; Lenhard, Boris (2015) GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics, 16 . ISSN 1471-2164

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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. Results and conclusion 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.

Item Type: Article
Additional Information: The authors would like to thank Thomas Carroll, Alexander Nash and Ge Tan for their helpful discussions during the development of this package, and the Bioconductor core team for their review and comments regarding the code and documentation of the package. NH, EI-S, MP and BL are funded by the Medical Research Council UK. AB and BL by EU project ZF-Health (FP7/2010-2015 grant agreement no 242048). MP by the Faculty of Medicine, Imperial College London. All authors contributed to the design and implementation of the package and the writing of the manuscript.
Uncontrolled Keywords: Bioconductor Package; Chromatin Interaction; Interaction Landscape; Enhancer Interaction; Individual Anchor
Subjects: INTERDISCIPLINARY AREAS OF KNOWLEDGE > Biotechnology in Biomedicine (natural science, biomedicine and healthcare, bioethics area
Divisions: UNSPECIFIED
Depositing User: Anja Barešić
Date Deposited: 28 Jul 2020 10:49
Last Modified: 28 Jul 2020 11:36
URI: http://fulir.irb.hr/id/eprint/5874
DOI: 10.1186/s12864-015-2140-x

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