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

Harmston, Nathan, Ing-Simmons, Elizabeth, Perry, Malcolm, Barešić, Anja and Lenhard, Boris 2015. GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics 16 (1) , 963. 10.1186/s12864-015-2140-x

Full text not available from this repository.

Abstract

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
Date Type:	Publication
Status:	Published
Schools:	Biosciences
ISSN:	1471-2164
Date of Acceptance:	23 October 2015
Last Modified:	25 Aug 2023 12:00
URI:	https://orca.cardiff.ac.uk/id/eprint/161874

Actions (repository staff only)

Edit Item