MethCP

DOI: 10.18129/B9.bioc.MethCP    

Differential methylation anlsysis for bisulfite sequencing data

Bioconductor version: Release (3.15)

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

PDF   Reference Manual

Details

biocViews DifferentialMethylation, Sequencing, Software, TimeCourse, WholeGenome
Version 1.10.0
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
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: