.png){kind=icon}
返回
DEBrowser: interactive differential expression analysis and visualization tool for count data
.png){kind=icon}
OA
AI
DOI：10.1186/s12864-018-5362-x.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
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.
Keyword:
Differential expression
Data visualization
Interactive data analysis
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
IF:
3.7
论文数:
1.9W
被引数:
5.2W
机构
引用论文
A Fixed-Point Neural Network Architecture for Speech Applications on Resource Constrained Hardware用于资源受限硬件上语音应用的定点神经网络体系结构
PREAI
分享收藏DEIVA: a web application for interactive visual analysis of differential gene expression profilesDEIVA：用于差异基因表达谱交互式可视化分析的Web应用.png)
BMC GENOMICSOAAI
BMC GENOMICSIF3.7
OAAI分享收藏A scaling normalization method for differential expression analysis of RNA-seq dataRna-seq数据差异表达分析的尺度归一化方法GENOME BIOLOGYOAAI
GENOME BIOLOGYIF9.4
OAAI分享收藏The PPARα-FGF21 Hormone Axis Contributes to Metabolic Regulation by the Hepatic JNK Signaling PathwayCELL METABOLISMOAAI
CELL METABOLISMIF30.9
OAAI分享收藏
查看更多内容