methylSig

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

MethylSig: Differential Methylation Testing for WGBS and RRBS Data

Bioconductor version: Development (3.24)

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")):

Yongseok Park, Raymond G. Cavalcante. methylSig: MethylSig: Differential Methylation Testing for WGBS and RRBS Data. doi:10.18129/B9.bioc.methylSig, R package version 1.25.13, https://bioconductor.org/packages/methylSig.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Regression, Sequencing, Software
Version	1.25.13
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	GPL-3
Depends	R (>= 4.5.0)
Imports	bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, Seqinfo, GenomicRanges, methods, parallel, stats, S4Vectors
System Requirements
URL	https://github.com/sartorlab/methylSig
Bug Reports	https://github.com/sartorlab/methylSig/issues

Suggests	BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 3.0.0), covr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	methylSig_1.25.13.tar.gz
Windows Binary (x86_64)	methylSig_1.25.13.zip (64-bit only)
macOS Binary (big-sur-x86_64)	methylSig_1.25.13.tgz
macOS Binary (sonoma-arm64)	methylSig_1.25.13.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