Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

countsTable | An Example Simulation Data |

drawMA_vol | Draw MA Plot and Volcano Plot |

ecdfAUC | Draw Empirical Cumulative Density Function (ECDF) plot |

equalSpace | Calculate Grouped Shrinkage Estimates |

exactNBtest1 | Perform only one exact test under the Negative Binomial... |

getAdjustDisp | Calculate Shrinkage (SH) Estimates for Dispersion |

getNormFactor | Estimate size factors |

getQ | Estimate the shrinkage target based on the quantiles of... |

getT | Estimate the shrinkage target based on the initial estimates |

getTgroup | This is an internal function used to calculate the shrinkage... |

Hammer2months | An example of real experiment. |

nbinomTestForMatricesSH | Exact test under Negative Binomial Test with Shrinkage... |

nbTestSH | Differential Analysis based on RNA-seq experiments using... |

plotDispersion | Drawing Dispersion-Mean plot. |

rnbinomMV | Randomly Generate Negative Binomial Variable with parameters... |

rowVars | Calculating the sample variance within each row of A matrix |

sim | Generating Simulated Data |

sSeq-package | Shrinkage estimation of dispersion in Negative Binomial... |

Sultan | An example of real experiment. |

Tuch | An example of real experiment. |

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