生物导体
计算机科学
可视化
R包
数据挖掘
聚类分析
样品(材料)
鉴定(生物学)
离群值
吞吐量
层次聚类
操作系统
程序设计语言
人工智能
生物
基因
植物
化学
无线
生物化学
色谱法
作者
Christopher Ward,Thu‐Hien To,Stephen Pederson
出处
期刊:Bioinformatics
[Oxford University Press]
日期:2019-12-16
卷期号:36 (8): 2587-2588
被引量:66
标识
DOI:10.1093/bioinformatics/btz937
摘要
Abstract Motivation High throughput next generation sequencing (NGS) has become exceedingly cheap, facilitating studies to be undertaken containing large sample numbers. Quality control (QC) is an essential stage during analytic pipelines and the outputs of popular bioinformatics tools such as FastQC and Picard can provide information on individual samples. Although these tools provide considerable power when carrying out QC, large sample numbers can make inspection of all samples and identification of systemic bias a challenge. Results We present ngsReports, an R package designed for the management and visualization of NGS reports from within an R environment. The available methods allow direct import into R of FastQC reports along with outputs from other tools. Visualization can be carried out across many samples using default, highly customizable plots with options to perform hierarchical clustering to quickly identify outlier libraries. Moreover, these can be displayed in an interactive shiny app or HTML report for ease of analysis. Availability and implementation The ngsReports package is available on Bioconductor and the GUI shiny app is available at https://github.com/UofABioinformaticsHub/shinyNgsreports. Supplementary information Supplementary data are available at Bioinformatics online.
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