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RnBeads 2.0: comprehensive analysis of DNA methylation data

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 implemen...

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Detalles Bibliográficos
Autores principales: Müller, Fabian, Scherer, Michael, Assenov, Yassen, Lutsik, Pavlo, Walter, Jörn, Lengauer, Thomas, Bock, Christoph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419383/
https://www.ncbi.nlm.nih.gov/pubmed/30871603
http://dx.doi.org/10.1186/s13059-019-1664-9
Descripción
Sumario: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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1664-9) contains supplementary material, which is available to authorized users.