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RADMeth specifications

Information


Unique identifier OMICS_07050
Name RADMeth
Alternative name Regression Analysis of Differential Methylation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Andrew Smith

Publication for Regression Analysis of Differential Methylation

RADMeth citations

 (8)
library_books

An information theoretic approach to the modeling and analysis of whole genome bisulfite sequencing data

2018
BMC Bioinformatics
PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5

[…] 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 […]

library_books

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR

2017
F1000Res
PMCID: 5747346
PMID: 29333247
DOI: 10.5256/f1000research.14317.r28483

[…] 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 […]

library_books

TEA: the epigenome platform for Arabidopsis methylome study

2016
BMC Genomics
PMCID: 5260138
PMID: 28155665
DOI: 10.1186/s12864-016-3326-6

[…] 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 […]

library_books

Information recovery from low coverage whole genome bisulfite sequencing

2016
Nat Commun
PMCID: 4931220
PMID: 27346250
DOI: 10.1038/ncomms11306

[…] –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 […]

library_books

Tet2 and Tet3 cooperate with B lineage transcription factors to regulate DNA modification and chromatin accessibility

2016
eLife
PMCID: 5142813
PMID: 27869616
DOI: 10.7554/eLife.18290.030

[…] 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 […]

library_books

Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

2015
Epigenomics
PMCID: 4790440
PMID: 26366945
DOI: 10.2217/epi.15.21

[…] 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 […]

Citations

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RADMeth institution(s)
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA

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