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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

Reference Manual PDF

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
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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
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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
Package Short Url https://bioconductor.org/packages/betaHMM/
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