An R package for gene and isoform differential expression analysis of RNA-seq data

beta.mom | Fit the beta distribution by method of moments |

crit_fun | Calculate the soft threshold for a target FDR |

DenNHist | Density plot to compare the empirical q's and the simulated... |

EBMultiTest | Using EM algorithm to calculate the posterior probabilities... |

EBSeq_NingLeng-package | EBSeq: RNA-Seq Differential Expression Analysis on both gene... |

EBTest | Using EM algorithm to calculate the posterior probabilities... |

f0 | The Prior Predictive Distribution of being EE |

f1 | The Prior Predictive Distribution of being DE |

GeneMat | The simulated data for two condition gene DE analysis |

GetDEResults | Obtain Differential Expression Analysis Results in a... |

GetMultiFC | Calculate the Fold Changes for Multiple Conditions |

GetMultiPP | Posterior Probability of Each Transcript |

GetNg | Ng Vector |

GetNormalizedMat | Calculate normalized expression matrix |

GetPatterns | Generate all possible patterns in a multiple condition study |

GetPP | Generate the Posterior Probability of each transcript. |

GetPPMat | Posterior Probability of Transcripts |

IsoList | The simulated data for two condition isoform DE analysis |

IsoMultiList | The simulated data for multiple condition isoform DE analysis |

Likefun | Likelihood Function of the NB-Beta Model |

LikefunMulti | Likelihood Function of the NB-Beta Model In Multiple... |

LogN | The function to run EM (one round) algorithm for the NB-beta... |

LogNMulti | EM algorithm for the NB-beta model in the multiple condition... |

MedianNorm | Median Normalization |

MultiGeneMat | The simulated data for multiple condition gene DE analysis |

PlotPattern | Visualize the patterns |

PlotPostVsRawFC | Plot Posterior FC vs FC |

PolyFitPlot | Fit the mean-var relationship using polynomial regression |

PostFC | Calculate the posterior fold change for each transcript... |

QQP | The Quantile-Quantile Plot to compare the empirical q's and... |

QuantileNorm | Quantile Normalization |

RankNorm | Rank Normalization |

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