Registration Open for Bioc2024 July 24-26


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

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

betaHMM HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, Coverage, DNAMethylation, DifferentialMethylation, GeneTarget, HiddenMarkovModel, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Sequencing, Software, Spatial
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
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
See More
Suggests rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
Linking To
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_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) betaHMM_1.0.0.tgz
macOS Binary (arm64) betaHMM_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats