This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

methylSig

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 (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("methylSig")

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

Documentation

Reference Manual PDF

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Regression, Software
Version 1.13.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 3.6)
Imports bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors
Linking To
Suggests BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr
System Requirements
Enhances
URL
Bug Reports https://github.com/sartorlab/methylSig/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary methylSig_1.13.0.zip
macOS Binary (x86_64) methylSig_1.13.0.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/
Package Downloads Report Download Stats