TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data
TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data
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DOI：
10.1186/s13104-019-4179-2
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发表时间：
2019-03-13
影响因子：
1.8
通讯作者：
Kadota, Koji
中科院分区：
文献类型：
--
作者：
Su, Wei;Sun, Jianqiang;Kadota, Koji
目的：差异表达(DE)是分析RNA-Seq计数数据的基本步骤。为此，我们以前开发了R/BioConductor组件(称为TCC)。虽然这个包具有内置健壮的归一化方法的独特功能，但到目前为止，它的使用仅限于R用户。因此，对于非R用户，需要一种替代TCC进行DE分析的方法。结果：在这里，我们提出了一个用于TCC的图形用户界面(称为TCC-GUI)。非R用户只需要Web浏览器作为其使用的最低要求(https://infinityloop.shinyapps.io/TCC-GUI/).TCC-图形用户界面在R中实现，并封装在闪亮的应用程序中。它包含了TCC的所有主要功能，包括具有稳健归一化功能的DE管道和各种条件下的模拟数据生成。它还包括(I)探索性分析工具，包括一个被称为平均轮廓的有用分数，用于衡量比较组的分离程度，(Ii)可视化工具，如火山图和具有等级聚类的热图，以及(Iii)使用R Markdown的报告工具。借助闪亮的图形用户界面框架，用户只需通过鼠标导航即可获得结果。Tcc-图形用户界面的源代码可以在麻省理工学院的许可下在https://github.com/swsoyee/TCC-GUI上找到。
Objective: Differential expression (DE) is a fundamental step in the analysis of RNA-Seq count data. We had previously developed an R/Bioconductor package (called TCC) for this purpose. While this package has the unique feature of an in-built robust normalization method, its use has so far been limited to R users only. There is thus, a need for an alternative to DE analysis by TCC for non-R users.Results: Here, we present a graphical user interface for TCC (called TCC-GUI). Non-R users only need a web browser as the minimum requirement for its use (https://infinityloop.shinyapps.io/TCC-GUI/). TCC-GUI is implemented in R and encapsulated in Shiny application. It contains all the major functionalities of TCC, including DE pipelines with robust normalization and simulation data generation under various conditions. It also contains (i) tools for exploratory analysis, including a useful score termed average silhouette that measures the degree of separation of compared groups, (ii) visualization tools such as volcano plot and heatmap with hierarchical clustering, and (iii) a reporting tool using R Markdown. By virtue of the Shiny-based GUI framework, users can obtain results simply by mouse navigation. The source code for TCC-GUI is available at https://github.com/swsoyee/TCC-GUI under MIT license.