Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments.
Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments.
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DOI：
10.12688/f1000research.8759.2
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
Ing-Simmons E
中科院分区：
文献类型：
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作者：
Lun AT;Perry M;Ing-Simmons E
通过染色质构象捕获和高通量测序（Hi-C）等技术，极大地促进了基因组相互作用的研究。这些全基因组实验产生了大量的数据，需要仔细分析才能获得有用的生物学结论。然而，由于缺乏基本的基础设施来表示和操纵基因组相互作用数据，因此阻碍了适当的软件工具的开发。在这里，我们介绍了InteractionSet包，它提供了表示基因组相互作用的类，并存储它们相关的实验数据，沿着这些类的低级操作和处理所需的方法。InteractionSet软件包利用了开源Bioconductor项目中的现有基础设施，同时又被设计用于更高级别分析的Bioconductor软件包使用。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。
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.