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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 (3.19)

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")):

Installation

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

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

browseVignettes("methylSig")
Updating methylSig code HTML R Script
Using methylSig HTML R Script
Reference Manual PDF
NEWS Text

Details

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
URL
Bug Reports https://github.com/sartorlab/methylSig/issues
See More
Suggests BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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/
Package Downloads Report Download Stats