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 (>= 4.5.0)
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
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-27 22:40:39 UTC
RemoteUrl: https://github.com/bioc/RhyME
RemoteRef: HEAD
RemoteSha: 4056e74f252c579012d8e50a38184876c52db72d
NeedsCompilation: yes
Packaged: 2026-11-08 15:57:05 UTC; root
Author: Yixiang Hong [aut, cre]
Maintainer: Yixiang Hong <yixiang.hong@uth.tmc.edu>