MethCP

Differential methylation anlsysis for bisulfite sequencing data

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("MethCP")):

Installation

To install this package, start R (version "4.3") 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


Reference Manual	PDF

Details

biocViews	DifferentialMethylation, Sequencing, Software, TimeCourse, WholeGenome
Version	1.13.0
In Bioconductor since	BioC 3.10 (R-3.6) (4 years)
License	Artistic-2.0
Depends	R (>= 3.6.0)
Imports	methods, utils, stats, S4Vectors, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel
Linking To
Suggests	testthat, knitr, rmarkdown
System Requirements
Enhances
URL
Bug Reports	https://github.com/boyinggong/methcp/issues

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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)	MethCP_1.13.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MethCP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MethCP
Bioc Package Browser	https://code.bioconductor.org/browse/MethCP/
Package Short Url	https://bioconductor.org/packages/MethCP/
Package Downloads Report	Download Stats