cellcyclegenes_whitfield2002
                        list of cell cycle genes identified in
                        Whitfield et al. 2002.
circ_dist               Pairwise distance between two circular
                        variables
cycle_npreg_insample    Obtain cyclic trend estimates from the training
                        data
cycle_npreg_loglik      Infer angles or cell cycle phase based on gene
                        expression data
cycle_npreg_mstep       Estimate parameters of the cyclic trends
cycle_npreg_outsample   Predict test-sample ordering using training
                        labels (no update)
data_transform_quantile
                        Transform counts by first computing
                        counts-per-million (CPM), then
                        quantile-normalize CPM for each gene
fit_bspline             Use bsplies to cyclic trend of gene expression
                        levels
fit_cyclical_many       Compute proportation of variance explained by
                        cyclic trends in the gene expression levels for
                        each gene.
fit_loess               Use loess to estimate cyclic trends of
                        expression values
fit_trendfilter         Using trendfiltering to estimate cyclic trend
                        of gene expression
initialize_grids        For prediction, initialize grid points for cell
                        cycle phase on a circle.
intensity2circle        Infer angles for each single-cell samples using
                        fluorescence intensities
model_5genes_predict    A SingleCellExperiment object
model_5genes_train      Traing model results among samples from 5
                        individuals.
rotation                Rotate circular variable shift_var to minimize
                        distance between ref_var and shift_var
sce_top101genes         Molecule counts of the 101 significant cyclical
                        genes in the 888 samples analyzed in the study.
shift_origin            Shift origin of the angles
training_human          Training data from 888 single-cell samples and
                        101 top cyclic genes
