betaHMM
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data
Bioconductor version: 3.23 · Package version: 1.8.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("betaHMM")Details
| Maintainer | Koyel Majumdar <koyelmajumdar.phdresearch@gmail.com> |
| Author | Koyel Majumdar [cre, aut] (ORCID: <https://orcid.org/0000-0001-6469-488X>), Romina Silva [aut], Antoinette Sabrina Perry [aut], Ronald William Watson [aut], Isobel Claire Gorley [aut] (ORCID: <https://orcid.org/0000-0001-7713-681X>), Thomas Brendan Murphy [aut] (ORCID: <https://orcid.org/0000-0002-5668-7046>), Florence Jaffrezic [aut], Andrea Rau [aut] (ORCID: <https://orcid.org/0000-0001-6469-488X>) |
| License | GPL-3 |
| Downloads rank | 184 |
| Source branch | RELEASE_3_23 |
| biocViews | BiomedicalInformatics, Coverage, DNAMethylation, DifferentialMethylation, GeneTarget, HiddenMarkovModel, ImmunoOncology, MethylationArray, Microarray, MultipleComparison, Sequencing, Software, Spatial |
Documentation
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Dependencies
Depends: R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges
Imports: stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle