DEBrowser: interactive differential expression analysis and visualization tool for count data
DEBrowser: interactive differential expression analysis and visualization tool for count data
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DOI：
10.1186/s12864-018-5362-x
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发表时间：
2019-01-05
期刊：
影响因子：
4.4
通讯作者：
Garber, Manuel
中科院分区：
文献类型：
--
作者：
Kucukural, Alper;Yukselen, Onur;Garber, Manuel
背景测序数据已成为衡量细胞活性的标准。例如，基因表达通过RNA测序（RNA-Seq）文库准确测量，蛋白质-DNA相互作用通过染色质免疫沉淀测序（ChIP-Seq）捕获，蛋白质-RNA相互作用通过交联免疫沉淀测序（CLIP-Seq）或RNA免疫沉淀（RIP-Seq）测序捕获，DNA可及性通过转座酶可及染色质（ATAC-Seq）、DNase或MNase测序文库的测定捕获。这些测序技术的处理涉及文库特异性方法。然而，在所有情况下，一旦测序文库被处理，结果是指定源自每个基因组基因座的读数的估计数目的计数表。用于确定哪些基因座在不同条件下具有不同细胞活性的差异分析从计数表开始，并通过数据评估、准备和分析的循环进行迭代。这种复杂的分析往往依赖于多个程序，因此对于那些没有编程技能的人来说是一个挑战。ResultsWe开发了DEBrowser作为R bioconductor项目，以交互方式可视化差分分析的每一步，而无需编程。该应用程序提供了一个基于R的闪亮基础设施的丰富的交互式Web图形用户界面。DEBrowser允许用户使用各种类型的图形来可视化数据，这些图形可以通过选择和重新绘制任何所需的数据子集来进一步探索。使用所提供的可视化方法，用户可以确定和纠正影响差异分析的技术变化，例如批次效应和测序深度。我们显示DEBrowser的易用性，通过再现两个先前公布的数据sets.ConclusionsDEBrowser的分析是一个灵活的，直观的，基于Web的分析平台，使计数数据的迭代和交互式分析，而无需任何编程知识的要求。
BackgroundSequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immunoprecipitation sequencing (CLIP-Seq) or RNA immunoprecipitation (RIP-Seq) sequencing, DNA accessibility by assay for transposase-accessible chromatin (ATAC-Seq), DNase or MNase sequencing libraries. The processing of these sequencing techniques involves library-specific approaches. However, in all cases, once the sequencing libraries are processed, the result is a count table specifying the estimated number of reads originating from each genomic locus. Differential analysis to determine which loci have different cellular activity under different conditions starts with the count table and iterates through a cycle of data assessment, preparation and analysis. Such complex analysis often relies on multiple programs and is therefore a challenge for those without programming skills.ResultsWe developed DEBrowser as an R bioconductor project to interactively visualize every step of the differential analysis, without programming. The application provides a rich and interactive web based graphical user interface built on R's shiny infrastructure. DEBrowser allows users to visualize data with various types of graphs that can be explored further by selecting and re-plotting any desired subset of data. Using the visualization approaches provided, users can determine and correct technical variations such as batch effects and sequencing depth that affect differential analysis. We show DEBrowser's ease of use by reproducing the analysis of two previously published data sets.ConclusionsDEBrowser is a flexible, intuitive, web-based analysis platform that enables an iterative and interactive analysis of count data without any requirement of programming knowledge.