AbsCor                  Calculate absolute correlations among gene
                        pairs
CalcMV                  Calculate estimated mean and variance of
                        RNA-Seq data
FlagCluster             Flag gene clusters with small within-cluster
                        phase differences and/or small within-cluster
                        sine scores
FormatSineOut           Format SinFun outputs from lists to matrix
ImpShift                Search for the optimal sample order by using
                        the Extended Nearest Insertion
NISFun                  Run Extended Nearest Insertion and 2-opt on a
                        gene cluster identified by OscopeKM function
NormForSine             Rescale the gene/isoform expression matrix
Opt2Shift               Run the 2-opt algorithm to improve the optimal
                        order searching of the Extended Nearest
                        Insertion
Oscope-package          Oscope - A statistical pipeline for identifying
                        oscillatory genes in unsynchronized single cell
                        RNA-seq
OscopeENI               Search for the optimal sample order for
                        different gene clusters
OscopeExampleData       Simulated gene level data set with 600 genes
                        and 30 cells.
OscopeKM                Oscope K medoid module
OscopeSine              Apply sine model on the full set of genes or
                        isoforms
PermuCut                Define sine scroe cutoff using permuted data
PipeR                   Calculate residual of polynomial fit
PipeShiftCDF            Calculate residual of the sliding polynomial
                        regression
scanK                   Run k-medoid algorithm with varying k on
                        similarity matrix
SineFun                 Apply sine model on one particular gene vs.
                        other genes
SineOptim               Function for searching optimal phase shift
