DMCHMM

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DMCHMM.

Differentially Methylated CpG using Hidden Markov Model


Bioconductor version: 3.9

A pipeline for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data.

Author: Farhad Shokoohi

Maintainer: Farhad Shokoohi <shokoohi at icloud.com>

Citation (from within R, enter citation("DMCHMM")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DMCHMM")

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("DMCHMM")
DMCHMM HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DifferentialMethylation, HiddenMarkovModel, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.5.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges, fdrtool
Imports utils, stats, grDevices, rtracklayer, multcomp, calibrate, graphics
System Requirements
URL
Bug Reports https://github.com/shokoohi/DMCHMM/issues
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Suggests testthat, knitr
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Package Archives

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

Source Package DMCHMM_1.6.0.tar.gz
Windows Binary DMCHMM_1.6.0.zip
Mac OS X 10.11 (El Capitan) DMCHMM_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DMCHMM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DMCHMM
Bioc Package Browser https://code.bioconductor.org/browse/DMCHMM/
Package Short Url https://bioconductor.org/packages/DMCHMM/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive