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BPRMeth: a flexible Bioconductor package for modelling methylation profiles.

ABSTRACT: High-throughput measurements of DNA methylation are increasingly becoming a mainstay of biomedical investigations. While the methylation status of individual cytosines can sometimes be informative, several recent papers have shown that the functional role of DNA methylation is better captured by a quantitative analysis of the spatial variation of methylation across a genomic region.Here, we present BPRMeth, a Bioconductor package that quantifies methylation profiles by generalized linear model regression. The original implementation has been enhanced in two important ways: we introduced a fast, variational inference approach that enables the quantification of Bayesian posterior confidence measures on the model, and we adapted the method to use several observation models, making it suitable for a diverse range of platforms including single-cell analyses and methylation arrays.http://bioconductor.org/packages/BPRMeth.Supplementary data are available at Bioinformatics online.

SUBMITTER: Kapourani CA

PROVIDER: S-EPMC6041802 | biostudies-other | 2018 Jul

REPOSITORIES: biostudies-other

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BPRMeth: a flexible Bioconductor package for modelling methylation profiles.

Kapourani Chantriolnt-Andreas CA Sanguinetti Guido G

Bioinformatics (Oxford, England) 20180701 14

<h4>Motivation</h4>High-throughput measurements of DNA methylation are increasingly becoming a mainstay of biomedical investigations. While the methylation status of individual cytosines can sometimes be informative, several recent papers have shown that the functional role of DNA methylation is better captured by a quantitative analysis of the spatial variation of methylation across a genomic region.<h4>Results</h4>Here, we present BPRMeth, a Bioconductor package that quantifies methylation pro ...[more]

PMID: 29522078

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