betaHMM

This is the released version of betaHMM; for the devel version, see betaHMM.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

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

Bioconductor version: Release (3.23)

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: 0000-0001-6469-488X , Romina Silva [aut], Antoinette Sabrina Perry [aut], Ronald William Watson [aut], Isobel Claire Gorley [aut] ORCID: 0000-0001-7713-681X , Thomas Brendan Murphy [aut] ORCID: 0000-0002-5668-7046 , Florence Jaffrezic [aut], Andrea Rau [aut] ORCID: 0000-0001-6469-488X

Maintainer: Koyel Majumdar <koyelmajumdar.phdresearch at gmail.com>

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

Koyel Majumdar, Romina Silva, Antoinette Sabrina Perry, Ronald William Watson, Isobel Claire Gorley, Thomas Brendan Murphy, Florence Jaffrezic, Andrea Rau. betaHMM: A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data. doi:10.18129/B9.bioc.betaHMM, R package version 1.8.0, https://bioconductor.org/packages/betaHMM.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

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	1.8.0
In Bioconductor since	BioC 3.19 (R-4.4) (2.5 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
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Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	betaHMM_1.8.0.tar.gz
Windows Binary (x86_64)	betaHMM_1.8.0.zip
macOS Binary (big-sur-x86_64)	betaHMM_1.8.0.tgz
macOS Binary (sonoma-arm64)	betaHMM_1.8.0.tgz
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/
Package Downloads Report	Download Stats