MethCP

DOI: 10.18129/B9.bioc.MethCP    

This is the development version of MethCP; for the stable release version, see MethCP.

Differential methylation anlsysis for bisulfite sequencing data

Bioconductor version: Development (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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
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, parallel, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb
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_1.1.0.tar.gz
Windows Binary MethCP_1.1.0.zip
Mac OS X 10.11 (El Capitan) MethCP_1.1.0.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

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