NEWS
RhyME 0.99.3
RhyME 0.99.2
- Respect the registered BiocParallel backend and prefix result columns with
RhyME_ to preserve existing row annotations.
- Add unit tests for automatic EB estimation, p-value separation, BH
adjustment, and phase recovery.
- Update the vignette with rhythmic and non-rhythmic examples, evaluated
automatic EB fits, MetaCycle comparisons, and methylation array input.
- Add real methylation CSV data and demonstrate constructing a
SummarizedExperiment from beta values and sample metadata.
- Declare MetaCycle and minfi in Suggests, and bundle the parameters and
sampling design needed to regenerate the example data.
- Use Bioconductor installation instructions in the README.
RhyME 0.99.1
- Replace TMB-based fitting with penalized quasi-likelihood (PQL), using a
null-model score test for rhythmicity and a separate full-model fit for
rhythm parameters.
RhyME 0.99.0
- Initial submission with TMB-based beta cosinor models, optional subject
random intercepts, and empirical Bayes precision shrinkage.