Quantifying Differential Rhythmicity based on Effect Sizes with LimoRhyde2

ABSTRACT Current methods for assessing differential rhythmicity in genomic data focus on hypothesis testing and model selection, often assuming sinusoidal rhythms. A more appropriate approach is to estimate differences in rhythmic properties between two or more conditions using effect sizes. To address this gap, we extend LimoRhyde2, a method for quantifying rhythm-related effect sizes and their uncertainty in genome-scale data, to enable differential rhythmicity analyses. Through extensive testing, we validate the method for differential rhythmicity analysis and showcase how it improves biological interpretation for circadian systems biology.