A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type

DOI10.1515/SAGMB-2016-0062MaRDI QIDQ1670290zbMATH OpenOpenAlexWikidataFDO

Authors Lajmi Lakhal-Chaieb, Celia M. T. Greenwood, Mohamed Ouhourane, Kaiqiong Zhao, Belkacem Abdous, Karim Oualkacha

Publication date 5 September 2018

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1515/sagmb-2016-0062

zbMATH Keywords

DNA methylationEM-algorithmkernel smoothingMethylC-SeqRRBS

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

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Cites work

• On Variable Bandwidth Selection in Local Polynomial Regression

Cited in

(8)

• Group penalized quantile regression
• \texttt{MLML2R}: an R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions
• Error correction in methylation profiling from NGS bisulfite protocols
• The cluster correlation-network support vector machine for high-dimensional binary classification
• A novel statistical method for modeling covariate effects in bisulfite sequencing derived measures of DNA methylation
• Addressing dispersion in mis-measured multivariate binomial outcomes: a novel statistical approach for detecting differentially methylated regions in bisulfite sequencing data
• A functional approach to testing overall effect of interaction between DNA methylation and SNPs
• Group penalized expectile regression

Describes a project that uses

Uses Software

• BSmooth
• BEAT

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