MethCP

This package is for version 3.11 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: 3.11

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 "4.0") 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 1.2.0
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
Links To Me
Build Report Build Report

Package Archives

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

Source Package MethCP_1.2.0.tar.gz
Windows Binary MethCP_1.2.0.zip
macOS 10.13 (High Sierra) MethCP_1.2.0.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 3.11 Source Archive