methylSig

DOI: 10.18129/B9.bioc.methylSig    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see methylSig.

MethylSig: Differential Methylation Testing for WGBS and RRBS Data

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

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

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Regression, Software
Version	1.4.0
In Bioconductor since	BioC 3.11 (R-4.0) (1.5 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors
LinkingTo
Suggests	BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr
SystemRequirements
Enhances
URL
BugReports	https://github.com/sartorlab/methylSig/issues
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	methylSig_1.4.0.tar.gz
Windows Binary	methylSig_1.4.0.zip
macOS 10.13 (High Sierra)	methylSig_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylSig
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylSig
Package Short Url	https://bioconductor.org/packages/methylSig/
Package Downloads Report	Download Stats