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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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:
Software
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
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author Müller, Fabian
Scherer, Michael
Assenov, Yassen
Lutsik, Pavlo
Walter, Jörn
Lengauer, Thomas
Bock, Christoph
author_facet Müller, Fabian
Scherer, Michael
Assenov, Yassen
Lutsik, Pavlo
Walter, Jörn
Lengauer, Thomas
Bock, Christoph
author_sort Müller, Fabian
collection PubMed
description 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.
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spelling pubmed-64193832019-03-27 RnBeads 2.0: comprehensive analysis of DNA methylation data Müller, Fabian Scherer, Michael Assenov, Yassen Lutsik, Pavlo Walter, Jörn Lengauer, Thomas Bock, Christoph Genome Biol Software 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. BioMed Central 2019-03-14 /pmc/articles/PMC6419383/ /pubmed/30871603 http://dx.doi.org/10.1186/s13059-019-1664-9 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Müller, Fabian
Scherer, Michael
Assenov, Yassen
Lutsik, Pavlo
Walter, Jörn
Lengauer, Thomas
Bock, Christoph
RnBeads 2.0: comprehensive analysis of DNA methylation data
title RnBeads 2.0: comprehensive analysis of DNA methylation data
title_full RnBeads 2.0: comprehensive analysis of DNA methylation data
title_fullStr RnBeads 2.0: comprehensive analysis of DNA methylation data
title_full_unstemmed RnBeads 2.0: comprehensive analysis of DNA methylation data
title_short RnBeads 2.0: comprehensive analysis of DNA methylation data
title_sort rnbeads 2.0: comprehensive analysis of dna methylation data
topic Software
url 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
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