RnBeads 2.0: comprehensive analysis of DNA methylation data
RnBeads 2.0: comprehensive analysis of DNA methylation data
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DOI：
10.1186/s13059-019-1664-9
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发表时间：
2019-03-14
期刊：
影响因子：
12.3
通讯作者：
Bock, Christoph
中科院分区：
文献类型：
--
作者：
Mueller, Fabian;Scherer, Michael;Bock, Christoph
DNA甲基化是一个被广泛研究的表观遗传标记，在发育和疾病中起着重要作用。高通量分析可以在大量样品中进行基因组规模的DNA甲基化分析。在这里，我们描述了我们的RnBeads软件的一个新版本——一个R/Bioconductor软件包，它实现了Infinium微阵列和各种亚硫酸盐测序的从头到尾分析工作流程。RnBeads 2.0 （https://rnbeads.org/）提供了额外的数据类型和分析方法，用于解释DNA甲基化差异的新功能，通过新颖的图形用户界面改进了可用性，并更好地利用了计算资源。我们在四个可重新运行的用例中演示了RnBeads 2.0，重点关注细胞分化和癌症。
DNA methylation is a widely investigated epigenetic mark with important roles in development and disease. High-throughput assays enable genome-scale DNA methylation analysis in large numbers of samples. Here, we describe a new version of our RnBeads software-an R/Bioconductor package that implements start-to-finish analysis workflows for Infinium microarrays and various types of bisulfite sequencing. RnBeads 2.0 (https://rnbeads.org/) provides additional data types and analysis methods, new functionality for interpreting DNA methylation differences, improved usability with a novel graphical user interface, and better use of computational resources. We demonstrate RnBeads 2.0 in four re-runnable use cases focusing on cell differentiation and cancer.