RnBeads 2.0: comprehensive analysis of DNA methylation data.

Fabian MüllerMichael SchererYassen AssenovPavlo LutsikJörn WalterThomas LengauerChristoph Bock

Published in: Genome biology (2019)

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.

Keyphrases

dna methylation
genome wide
gene expression
high throughput
electronic health record
single cell
copy number
big data
high resolution
social media
artificial intelligence
single molecule