Integrated genome browser: visual analytics platform for genomics.
Integrated genome browser: visual analytics platform for genomics.
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DOI：
10.1093/bioinformatics/btw069
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发表时间：
2016-07-15
期刊：
影响因子：
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通讯作者：
Loraine AE
中科院分区：
文献类型：
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作者：
Freese NH;Norris DC;Loraine AE
动机：基因组浏览器支持在大量数据集中快速导航，并提供交互式可视化分析功能，可以帮助科学家更深入地了解生物系统。为此，我们开发了集成基因组浏览器（IGB），这是一个高度可配置、交互式和快速的开源桌面基因组浏览器。结果：在这里，我们描述了对IGB的多个更新，包括显示和与高通量测序实验数据交互的全新功能。为了证明这一点，我们描述了来自RNA-Seq， ChIP-Seq和亚硫酸盐测序实验的数据集的可视化和分析示例。理解基因组规模实验的结果需要在参考基因组注释和其他相关数据集的背景下查看数据。为了实现这一点，我们增强了IGB使用来自不同来源的数据的能力，包括Galaxy、分布式注释和特定于IGB的Quickload服务器。随着新的基因组规模分析的广泛应用，为了支持未来的可视化需求，我们将IGB代码库转换为一个模块化的、可扩展的平台，供开发人员创建和部署全新的基因组数据可视化。可用性和实现：IGB是开源的，可以从http://bioviz.org/igb免费获得。联系:aloraine@uncc.edu
Motivation: Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Results: Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB’s ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. Availability and implementation: IGB is open source and is freely available from http://bioviz.org/igb. Contact: aloraine@uncc.edu