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This is the development version of methylSig; for the stable release version, see methylSig.

MethylSig: Differential Methylation Testing for WGBS and RRBS Data

Bioconductor version: Development (3.19)

MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.

Author: Yongseok Park [aut], Raymond G. Cavalcante [aut, cre]

Maintainer: Raymond G. Cavalcante <rcavalca at umich.edu>

Citation (from within R, enter citation("methylSig")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Updating methylSig code HTML R Script
Using methylSig HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Regression, Software
Version 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends R (>= 3.6)
Imports bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors
System Requirements
Bug Reports https://github.com/sartorlab/methylSig/issues
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Suggests BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr
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Follow Installation instructions to use this package in your R session.

Source Package methylSig_1.15.0.tar.gz
Windows Binary methylSig_1.15.0.zip
macOS Binary (x86_64) methylSig_1.15.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/methylSig
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methylSig
Bioc Package Browser https://code.bioconductor.org/browse/methylSig/
Package Short Url https://bioconductor.org/packages/methylSig/
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