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cff-version: 1.2.0
message: 'To cite package "RhyME" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'RhyME: Beta Regression Cosinor Models for Circadian Methylation Analysis'
version: 0.99.0
doi: 10.32614/CRAN.package.RhyME
abstract: 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.
authors:
- family-names: Hong
  given-names: Yixiang
  email: yixiang.hong@uth.tmc.edu
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/njuelsdke/RhyME
commit: cbe5289e2a0654fc81e8caebc24950e14c84b351
url: https://github.com/njuelsdke/RhyME
date-released: '2026-08-21'
contact:
- family-names: Hong
  given-names: Yixiang
  email: yixiang.hong@uth.tmc.edu