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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Bibliographic Details
Published in:Genome Biology Vol. 20; no. 1; p. 55
Main Authors: Müller, Fabian, Scherer, Michael, Assenov, Yassen, Lutsik, Pavlo, Walter, Jörn, Lengauer, Thomas, Bock, Christoph
Format: Journal Article
Language:English
Published: London BioMed Central 14.03.2019
Springer Nature B.V
BMC
Subjects:
Adolescent
Adult
Age Factors
Aged
Aged, 80 and over
Animal Genetics and Genomics
Bioinformatics
Biomarkers, Tumor - genetics
Biomedical and Life Sciences
Bisulfite
Bisulfite sequencing
bisulfites
Cancer
cell differentiation
Child
Computational Biology - methods
Computational epigenetics
Computer applications
computer software
Data analysis
Data processing
Datasets
Deoxyribonucleic acid
DNA
DNA Methylation
DNA microarrays
Embryonic Stem Cells - cytology
Embryonic Stem Cells - metabolism
Epigenetics
Epigenome-wide association studies
Epigenomics
Epigenotyping microarrays
Evolutionary Biology
Female
genome
Genome, Human
Genomes
High-Throughput Nucleotide Sequencing
Human Genetics
Humans
Integrative data analysis
Life Sciences
Male
microarray technology
Microbial Genetics and Genomics
Middle Aged
Neoplasms - genetics
Plant Genetics and Genomics
Sequence Analysis, DNA - methods
Sex Factors
Software
Software packages
User interface
Young Adult
Integrative data analysis
R/Bioconductor package
Bisulfite sequencing
DNA methylation
Epigenotyping microarrays
Epigenome-wide association studies
Computational epigenetics
Bioinformatics software tool
ISSN:1474-760X, 1474-7596, 1474-760X
Online Access:Get full text
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Description
Summary: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.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-019-1664-9