MethCP

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MethCP.

Differential methylation anlsysis for bisulfite sequencing data


Bioconductor version: 3.16

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 "4.2") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MethCP")
methcp: User’s Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialMethylation, Sequencing, Software, TimeCourse, WholeGenome
Version 1.11.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License Artistic-2.0
Depends R (>= 3.6.0)
Imports methods, utils, stats, S4Vectors, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel
System Requirements
URL
Bug Reports https://github.com/boyinggong/methcp/issues
See More
Suggests testthat, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package MethCP_1.11.0.tar.gz
Windows Binary MethCP_1.11.0.zip
macOS Binary (x86_64) MethCP_1.11.0.tgz
macOS Binary (arm64) MethCP_1.12.0.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
Old Source Packages for BioC 3.16 Source Archive