MethCP

DOI: 10.18129/B9.bioc.MethCP    

Differential methylation anlsysis for bisulfite sequencing data

Bioconductor version: Release (3.14)

MethCP is a differentially methylated region (DMR) detecting method for whole-genome bisulfite sequencing (WGBS) data, which is applicable for a wide range of experimental designs beyond the two-group comparisons, such as time-course data. MethCP identifies DMRs based on change point detection, which naturally segments the genome and provides region-level differential analysis.

Author: Boying Gong [aut, cre]

Maintainer: Boying Gong <jorothy_gong at berkeley.edu>

Installation

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

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

BiocManager::install("MethCP")

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

Documentation

PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialMethylation, Sequencing, Software, TimeCourse, WholeGenome
Version	1.8.0
In Bioconductor since	BioC 3.10 (R-3.6) (2.5 years)
License	Artistic-2.0
Depends	R (>= 3.6.0)
Imports	methods, utils, stats, S4Vectors, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel
LinkingTo
Suggests	testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/boyinggong/methcp/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
Windows Binary	MethCP_1.8.0.zip
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/MethCP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MethCP
Package Short Url	https://bioconductor.org/packages/MethCP/
Package Downloads Report	Download Stats