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RnBeads 2.0: comprehensive analysis of DNA methylation data.


ABSTRACT: 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.

SUBMITTER: Muller F 

PROVIDER: S-EPMC6419383 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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RnBeads 2.0: comprehensive analysis of DNA methylation data.

Müller Fabian F   Scherer Michael M   Assenov Yassen Y   Lutsik Pavlo P   Walter Jörn J   Lengauer Thomas T   Bock Christoph C  

Genome biology 20190314 1


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  ...[more]

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