Lun Aaron T L, Perry Malcolm, Ing-Simmons Elizabeth
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK.
F1000Res. 2016 May 20;5:950. doi: 10.12688/f1000research.8759.2. eCollection 2016.
The 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 InteractionSet 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 InteractionSet 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 InteractionSet will simplify development, allow access to more features and improve interoperability between packages.
诸如高通量测序染色质构象捕获技术（Hi-C）极大地推动了基因组相互作用的研究。这些全基因组实验产生了大量数据，需要仔细分析才能得出有用的生物学结论。然而，由于缺乏表示和处理基因组相互作用数据的基础架构，合适软件工具的开发受到了阻碍。在这里，我们展示了InteractionSet软件包，它提供了用于表示基因组相互作用并存储其相关实验数据的类，以及对这些类进行底层操作和处理所需的方法。InteractionSet软件包利用了开源Bioconductor项目中的现有基础架构，反过来又被用于更高层次分析的Bioconductor软件包所使用。对于新软件包，使用InteractionSet中的功能将简化开发，允许访问更多功能并提高软件包之间的互操作性。
