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... |

FormatSineOut | Format SinFun outputs from lists to matrix |

ImpShift | Search for the optimal sample order by using the Extended... |

NISFun | Run Extended Nearest Insertion and 2-opt on a gene cluster... |

NormForSine | Rescale the gene/isoform expression matrix |

Opt2Shift | Run the 2-opt algorithm to improve the optimal order... |

OscopeENI | Search for the optimal sample order for different gene... |

OscopeExampleData | Simulated gene level data set with 600 genes and 30 cells. |

OscopeKM | Oscope K medoid module |

Oscope-package | Oscope - A statistical pipeline for identifying oscillatory... |

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 |

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