Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

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Documentation for package ‘Oscope’ version 1.38.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.
• Package NEWS.

Help Pages

Oscope-package	Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
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	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