MethCP

DOI: 10.18129/B9.bioc.MethCP    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MethCP.

Differential methylation anlsysis for bisulfite sequencing data

Bioconductor version: 3.10

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 "3.6") and enter:

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

BiocManager::install("MethCP")

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("MethCP")

 

HTML	R Script	methcp: User’s Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialMethylation, Sequencing, Software, TimeCourse, WholeGenome
Version	1.0.2
In Bioconductor since	BioC 3.10 (R-3.6) (< 6 months)
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	MethCP_1.0.2.tar.gz
Windows Binary	MethCP_1.0.0.zip
Mac OS X 10.11 (El Capitan)	MethCP_1.0.2.tgz
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