Models continuous temporal trajectories from BULK or time-resolved omics where the x-axis is measured experimental time: penalized GAMs (mgcv) for smooth trends and changepoint detection (segmented, ruptures) for abrupt regime shifts. Use when deciding between a smooth GAM and a changepoint model; choosing the GAM distribution (nb() plus a library-size offset for raw counts vs Gaussian on vst/log-CPM); setting the basis-dimension ceiling k below the number of timepoints and letting REML pick wiggliness; handling residual autocorrelation across timepoints with corAR1/bam(rho=); testing whether two conditions' trajectories diverge with an ordered-factor difference smooth; a…
