Package: RhyME 0.99.0

Yixiang Hong

RhyME: Beta Regression Cosinor Models for Circadian Methylation Analysis

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:Yixiang Hong [aut, cre]

RhyME_0.99.0.tar.gz
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RhyME_0.99.0.tgz(r-4.6-x86_64)RhyME_0.99.0.tgz(r-4.6-arm64)RhyME_0.99.0.tgz(r-4.5-x86_64)RhyME_0.99.0.tgz(r-4.5-arm64)
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RhyME_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
RhyME/json (API)

# Install 'RhyME' in R:

install.packages('RhyME', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/njuelsdke/rhyme/issues

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

epigenetics dnamethylation timecourse regression differentialmethylation software cpp openmp

3.00 score 3 exports 45 dependencies

Last updated from:cbe5289e2a. Checks:1 NOTE, 15 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	280
linux-devel-arm64	OK	315
linux-devel-x86_64	OK	383
source / vignettes	OK	355
linux-release-arm64	OK	320
linux-release-x86_64	OK	365
macos-release-arm64	OK	224
macos-release-x86_64	OK	665
macos-oldrel-arm64	OK	255
macos-oldrel-x86_64	OK	565
windows-devel-arm64	OK	422
windows-devel-x86_64	OK	365
windows-release-arm64	OK	387
windows-release-x86_64	OK	349
windows-oldrel-x86_64	OK	290
wasm-release	OK	181