betaHMM
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 ucdconnect.ie>
citation("betaHMM")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| 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 | |
| URL |
See More
| Suggests | rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| 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 (x86_64) | betaHMM_1.0.0.zip |
| macOS Binary (x86_64) | betaHMM_1.0.0.tgz |
| macOS Binary (arm64) | betaHMM_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/betaHMM |
| Source Repository (Developer Access) | git clone [email protected]:packages/betaHMM |
| Bioc Package Browser | https://code.bioconductor.org/browse/betaHMM/ |
| Package Short Url | https://bioconductor.org/packages/betaHMM/ |
| Package Downloads Report | Download Stats |