RADMeth

[…] o statistically determine methylation differences at individual CpG sites. One such recent method, known as DSS [, ], has been compared to several methods (such as methylKit [], BSmooth [], BiSeq [], RADMeth [], and MOABS []), using simulated as well as real data and has been found to be more preferable than these methods. Moreover, metilene, a recently proposed DMR finder [], was found to be supe […]

[…] ce modelling. For example, DSS fits a Bayesian hierarchical beta-binomial model to BS-seq data and uses Wald tests to detect DMRs . Other software using beta-binomial model include BiSeq , MOABS and RADMeth .In this workflow, we demonstrate an edgeR approach of differential methylation analysis. edgeR is one of the most popular Bioconductor packages for assessing differential expression in RNA-se […]

[…] each C in the genome. Tools have been developed to deal with whole-genome BS-Seq (WGBS) data, such as BiSeq [], BSmooth [], DMAP [], methPipe [], methylKit [], methylPipe [], methylSig [], MOABS [], radMeth [], and WBSA []. Most of these analysis tools focus on identifying differentially methylated regions (DMRs) and defining differentially methylated genes (DMGs) as genes with DMRs in or near th […]

[…] –10 against deep replicates M1–2 as part of a separate saturation analysis. For each methylome, the number of iCGs, DMPs, DMRs, COMETs and DMCs was determined. Two established algorithms (BSmooth and RADmeth) were used for DMR and DMP calling respectively, while COMETvintage was used for DMC calling (, Methods). COMETvintage uses the COMET distributions () as a count matrix with fixed windows appl […]

[…] We used Regression Analysis of Differential Methylation (RADMeth; methpipe V.3.4.2) () for computing individual differentially methylated sites with the regression command, and posterior grouping into differentially methylated regions (DMRs) with the adjust […]

[…] h condition, they need to be pooled first where biological variability is lost. MOABS identifies DMCs using beta-binomial hierarchical model and groups these into DMRs using a Hidden Markov Model []. Radmeth [] identifies DMCs by beta-binomial regression and detects DMRs by jointing neighboring DMCs with p-value below user-defined threshold where regional statistics (such as log odds ratio and mea […]