Circadian Oscillation Detection Analysis and Comparison (CODAC): a Multicriteria Method to Estimate and Compare Rhythmicity

Analysis of circadian patterns in time-series data requires computational methods that can accommodate several factors, including variable sampling resolution, replicate number, and missing values. Most existing tools simplify rhythmicity to a strict dichotomy based solely on a single p-value threshold. This leads to a level of uncertainty that affects many biological targets. We developed CODAC (Circadian Oscillation Detection Analysis and Comparison), a framework that integrates nonlinear constrained optimization with a multicriteria rhythmicity classification scheme to evaluate rhythmic patterns without relying on a single statistical cutoff. This approach allows CODAC to identify and exclude medium-confidence rhythms rather than force them into a rhythmic/arrhythmic dichotomy. CODAC comprises four modules: (i) CODAC_single estimates rhythmicity within a single group; (ii) CODAC_flex extends this to identify distinct waveform types within one group; (iii) CODAC_compare performs pairwise comparisons across two or more groups to detect rhythmic or arrhythmic changes; and (iv) CODAC_multi handles more complex designs involving multiple-group comparisons. Using in silico simulations and public transcriptomic datasets, we show that CODAC performs comparably to established methods while providing additional flexibility for rhythm classification and comparison. Taken together, CODAC provides a flexible and open-source package for circadian timeseries analysis with automated visualization tools.