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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

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

Suggests	BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr
Linking To
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Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/methylSig/
Package Downloads Report	Download Stats