Package: RhyME
Title: Beta Regression Cosinor Models for Circadian Methylation
        Analysis
Version: 0.99.0
Authors@R: person("Yixiang", "Hong",
    email = "yixiang.hong@uth.tmc.edu", role = c("aut", "cre"))
Description: Fits cosinor-based beta regression models for detecting
        circadian rhythmicity in DNA methylation array data using
        Template Model Builder (TMB) for efficient likelihood
        optimization. Supports fixed-effects (cross-sectional) and
        mixed-effects (repeated measures) designs with configurable
        period and adjustment covariates. Implements empirical Bayes
        shrinkage of the beta distribution precision parameter across
        CpG sites, analogous to limma's moderated variance, to improve
        genome-wide inference. Provides amplitude, phase, and MESOR
        estimation on both logit-link and response scales.
License: GPL (>= 3) + file LICENSE
URL: https://github.com/njuelsdke/RhyME
BugReports: https://github.com/njuelsdke/RhyME/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
biocViews: Epigenetics, DNAMethylation, TimeCourse, Regression,
        DifferentialMethylation, Software
Depends: R (>= 4.3.0)
Imports: SummarizedExperiment, S4Vectors, BiocParallel, TMB, stats,
        ggplot2
LinkingTo: TMB, RcppEigen
Suggests: knitr, rmarkdown, BiocStyle, BiocGenerics, RUnit, limma,
        cowplot
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-08-21 22:32:49 UTC
RemoteUrl: https://github.com/BiocStaging/RhyME
RemoteRef: HEAD
RemoteSha: cbe5289e2a0654fc81e8caebc24950e14c84b351
NeedsCompilation: yes
Packaged: 2026-09-21 06:53:29 UTC; root
Author: Yixiang Hong [aut, cre]
Maintainer: Yixiang Hong <yixiang.hong@uth.tmc.edu>