betaHMM

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

A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

Bioconductor version: Development (3.21)

A novel approach utilizing a homogeneous hidden Markov model. And effectively model untransformed beta values. To identify DMCs while considering the spatial. Correlation of the adjacent CpG sites.

Author: Koyel Majumdar [cre, aut] (ORCID: ), Romina Silva [aut], Antoinette Sabrina Perry [aut], Ronald William Watson [aut], Isobel Claire Gorley [aut] (ORCID: ), Thomas Brendan Murphy [aut] (ORCID: ), Florence Jaffrezic [aut], Andrea Rau [aut] (ORCID: )

Maintainer: Koyel Majumdar <koyel.majumdar at ucdconnect.ie>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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

BiocManager::install("betaHMM")

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("betaHMM")

betaHMM	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, Coverage, DNAMethylation, DifferentialMethylation, GeneTarget, HiddenMarkovModel, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Sequencing, Software, Spatial
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	GPL-3
Depends	R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges
Imports	stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils
System Requirements
URL

Suggests	rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
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.

Source Package	betaHMM_1.3.0.tar.gz
Windows Binary (x86_64)	betaHMM_1.3.0.zip
macOS Binary (x86_64)	betaHMM_1.3.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/betaHMM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/betaHMM
Bioc Package Browser	https://code.bioconductor.org/browse/betaHMM/
Package Short Url	https://bioconductor.org/packages/betaHMM/
Package Downloads Report	Download Stats