ggcoverage:一个R包,用于可视化和注释各种NGS数据的基因组覆盖面.
1School of Life Sciences, Tsinghua University, Beijing, China. songyb18@mails.tsinghua.edu.cn.
BMC bioinformatics
|August 9, 2023
概括
ggcoverage是一个新的R包,用于可视化和注释下一代测序 (NGS) 数据. 它为跨多个组和omics的基因组覆盖图提供了灵活性和定制性,改善了数据解释.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 可视化基因组覆盖面对于解释下一代测序 (NGS) 数据至关重要.
- 整合基因组注释与覆盖数据存在挑战,因为不同的NGS数据类型和注释要求.
- 现有的可视化工具往往缺乏灵活性,用户友好性和全面的注释功能.
研究的目的:
- 引入ggcoverage,一个R包,旨在灵活和高效的可视化和多组和多组基因组覆盖的注释.
- 提供一个用户友好的解决方案,通过提供强大的预处理和广泛的注释选项来克服现有工具的局限性.
主要方法:
- 开发了ggcoverage作为一个支持BAM,BigWig,BedGraph和TSV输入格式的R包.
- 集成的最先进的工具用于读取规范化,共识峰值生成和跟踪数据加载.
- 可以轻松叠加各种注释 (例如,对于WGS/WES,RNA-seq,ChIP-seq) 和蛋白质覆盖率可视化.
主要成果:
- ggcoverage 简化了对多组和多组数据的基因组覆盖率的可视化和注释.
- 该软件包提供了高效的预处理功能,包括读取规范化和共识峰值生成.
- 生成的图表具有出版质量,可以使用ggplot2进行定制,支持各种NGS数据类型和蛋白质覆盖.
结论:
- ggcoverage提供了一种灵活,可编程,高效和用户友好的解决方案,用于可视化和注释基因组覆盖范围.
- 该包增强了复杂的基因组和多基因组数据集的解释.
- ggcoverage 在GitHub上提供了全面的视频,用于用户指导.
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