Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA and Department of Statistics, University of California at Davis, Davis, CA 95616, USA.
Bioinformatics. 2013 Dec 15;29(24):3220-1. doi: 10.1093/bioinformatics/btt551. Epub 2013 Sep 29.
It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API.
The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.
计算分析通常会生成大量复杂数据，这些数据难以处理和与合作者共享。需要标准的方法将此类数据转换为更有用和直观的格式。我们介绍了 ReportingTools，这是一个 Bioconductor 软件包，它可以自动识别和转换许多常见的 Bioconductor 软件包的输出，生成丰富的、交互式的基于 HTML 的报告。报告不是通用的，而是根据检测到的结果类型单独设计的，以反映特定内容。报告中包含的表格输出可排序、可筛选和可搜索，并包含与上下文相关的外部数据库超链接。此外，还为特定的分析类型开发了嵌入式图形，并在默认情况下嵌入到表格行中，为基础原始数据提供了有用的可视化摘要。ReportingTools 非常灵活，可以使用定义良好的 API 轻松针对特定应用程序自定义报告。
ReportingTools 软件包是用 R 实现的，并可从 Bioconductor（版本≥2.11）获得，网址为：http://bioconductor.org/packages/release/bioc/html/ReportingTools.html。也可以在上述网址找到安装说明和使用文档。
