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Bioconductor - MethCP

MethCP

This package is for version 3.10 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: 3.10

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>

Citation (from within R, enter citation("MethCP")): Installation

To install this package, start R (version "3.6") 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")
Details biocViews DifferentialMethylation, Sequencing, Software, TimeCourse, WholeGenome Version 1.0.2 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.


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