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betaHMM

This is the development version of betaHMM; to use it, please install the devel version of Bioconductor.

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


Bioconductor version: Development (3.19)

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] , Romina Silva [aut], Antoinette Sabrina Perry [aut], Ronald William Watson [aut], Isobel Claire Gorley [aut] , Thomas Brendan Murphy [aut] , Florence Jaffrezic [aut], Andrea Rau [aut]

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

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews BiomedicalInformatics, Coverage, DNAMethylation, DifferentialMethylation, GeneTarget, HiddenMarkovModel, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Sequencing, Software, Spatial
Version 0.99.5
In Bioconductor since BioC 3.19 (R-4.4)
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
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Suggests rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
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Package Archives

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

Source Package betaHMM_0.99.5.tar.gz
Windows Binary betaHMM_0.99.5.zip
macOS Binary (x86_64) betaHMM_0.99.5.tgz
macOS Binary (arm64) betaHMM_0.99.5.tgz
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