circaTime - Unified Inference of Circadian Phase from Bulk and Pseudobulk Transcriptomes

Provides a single SummarizedExperiment-based interface to published circadian phase (time-of-sample-collection) inference methods for bulk and donor-level pseudobulk transcriptomes, along with a shared cross-validation benchmarking harness, cross-dataset transfer testing, and a calibrated uncertainty layer: bootstrap and Bayesian confidence intervals validated for real coverage, a fixed or dynamically-selected clock-gene quality flag, and consensus phase estimation across every bundled engine. Does not implement a new phase-inference algorithm; unifies existing published methods that are otherwise scattered across incompatible standalone implementations.