betaHMM
This is the released version of betaHMM; for the devel version, see betaHMM.
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]
, 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 <koyelmajumdar.phdresearch at gmail.com>
citation("betaHMM")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
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 |
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_1.8.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/betaHMM/ |
| Package Short Url | https://bioconductor.org/packages/betaHMM/ |
| Package Downloads Report | Download Stats |