RhyME
This is the development version of RhyME; to use it, please install the devel version of Bioconductor.
Beta Regression Cosinor Models for Circadian Methylation Analysis
Bioconductor version: Development (3.24)
Fits beta cosinor models to methylation measurements using penalized quasi-likelihood (PQL), an optional subject random intercept, adjustment covariates, and an optional empirical Bayes (EB) prior on log precision. Tests rhythmicity with a null-model score test and estimates rhythm parameters from a separate full-model fit.
Author: Yixiang Hong [aut, cre]
Maintainer: Yixiang Hong <yixiang.hong at uth.tmc.edu>
citation("RhyME")):Yixiang Hong. RhyME: Beta Regression Cosinor Models for Circadian Methylation Analysis. doi:10.18129/B9.bioc.RhyME, R package version 0.99.3, https://bioconductor.org/packages/RhyME.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("RhyME")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("RhyME")| Using RhyME for circadian methylation analysis | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, MethylationArray, Regression, Software, TimeCourse |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5.0) |
| Imports | Rcpp, SummarizedExperiment, S4Vectors, BiocParallel, stats, ggplot2, withr |
| System Requirements | C++17 |
| URL | https://github.com/njuelsdke/RhyME |
| Bug Reports | https://github.com/njuelsdke/RhyME/issues |
See More
| Suggests | MetaCycle, minfi, knitr, rmarkdown, BiocStyle, BiocGenerics, RUnit |
| Linking To | Rcpp, RcppEigen, BH |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/RhyME |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RhyME |
| Package Short Url | https://bioconductor.org/packages/RhyME/ |
| Package Downloads Report | Download Stats |