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Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments [version 1; referees: 2 approved]

Published version
Peer-reviewed

Type

Article

Change log

Authors

Lun, ATL 
Perry, M 
Ing-Simmons, E 

Abstract

ns4:pThe study of genomic interactions has been greatly facilitated by techniques such as chromatin conformation capture with high-throughput sequencing (Hi-C). These genome-wide experiments generate large amounts of data that require careful analysis to obtain useful biological conclusions. However, development of the appropriate software tools is hindered by the lack of basic infrastructure to represent and manipulate genomic interaction data. Here, we present the ns4:italicInteractionSet</ns4:italic> package that provides classes to represent genomic interactions and store their associated experimental data, along with the methods required for low-level manipulation and processing of those classes. The ns4:italicInteractionSet </ns4:italic>package exploits existing infrastructure in the open-source Bioconductor project, while in turn being used by Bioconductor packages designed for higher-level analyses. For new packages, use of the functionality in ns4:italicInteractionSet</ns4:italic> will simplify development, allow access to more features and improve interoperability between packages.</ns4:p>

Description

Keywords

31 Biological Sciences, 3102 Bioinformatics and Computational Biology, 3105 Genetics, Human Genome, Genetics, Networking and Information Technology R&D (NITRD)

Journal Title

F1000Research

Conference Name

Journal ISSN

2046-1402
1759-796X

Volume Title

5

Publisher

F1000 Research Ltd
Sponsorship
Cancer Research UK (Grant ID: A17197)