DMCHMM

DOI: 10.18129/B9.bioc.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>

Installation

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

if (!requireNamespace("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")

 

HTML	R Script	DMCHMM
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DifferentialMethylation, HiddenMarkovModel, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	GPL-3
Depends	R (>= 3.5.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges, fdrtool
Imports	utils, stats, grDevices, rtracklayer, multcomp, calibrate, graphics
LinkingTo
Suggests	testthat, knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/shokoohi/DMCHMM/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	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
Package Short Url	https://bioconductor.org/packages/DMCHMM/
Package Downloads Report	Download Stats