Package: RhyME
Title: Beta Regression Cosinor Models for Circadian Methylation
        Analysis
Version: 0.99.3
Authors@R: person("Yixiang", "Hong", email = "yixiang.hong@uth.tmc.edu",
    role = c("aut", "cre"))
Description: 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.
License: GPL (>= 3)
URL: https://github.com/njuelsdke/RhyME
BugReports: https://github.com/njuelsdke/RhyME/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
biocViews: Epigenetics, DNAMethylation, MethylationArray, TimeCourse,
        Regression, DifferentialMethylation
Depends: R (>= 4.6.0)
Imports: Rcpp, SummarizedExperiment, S4Vectors, BiocParallel, stats,
        ggplot2, withr
LinkingTo: Rcpp, RcppEigen, BH
Suggests: MetaCycle, minfi, knitr, rmarkdown, BiocStyle, BiocGenerics,
        RUnit
VignetteBuilder: knitr
SystemRequirements: C++17
Config/roxygen2/version: 8.1.0
git_url: https://git.bioconductor.org/packages/RhyME
git_branch: devel
git_last_commit: 4056e74
git_last_commit_date: 2026-10-27
Repository: Bioconductor 3.24
Date/Publication: 2026-11-08
NeedsCompilation: yes
Packaged: 2026-11-09 01:24:02 UTC; biocbuild
Author: Yixiang Hong [aut, cre]
Maintainer: Yixiang Hong <yixiang.hong@uth.tmc.edu>
