betaHMM
This is the development version of betaHMM; for the stable release version, see betaHMM.
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data
Bioconductor version: Development (3.20)
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")
# 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
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 | 1.1.0 |
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_1.1.0.tar.gz |
Windows Binary | betaHMM_1.1.0.zip |
macOS Binary (x86_64) | betaHMM_1.1.0.tgz |
macOS Binary (arm64) | betaHMM_1.1.0.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 |