betaHMM

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see betaHMM.

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

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

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

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")
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 1.4.2

In Bioconductor since BioC 3.19 (R-4.4) (1.5 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

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Build Report Build Report

Package Archives

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

Source Package betaHMM_1.4.2.tar.gz

Windows Binary (x86_64) betaHMM_1.4.1.zip

macOS Binary (x86_64) betaHMM_1.4.2.tgz

macOS Binary (arm64) betaHMM_1.4.2.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

Old Source Packages for BioC 3.21 Source Archive