Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

beta.mom | Method of moments estimation ( beta distribution ) |

EBHMMNBfun | Baum-Welch algorithm for a single hidden markov chain |

EBHMMNBfunForMulti | Baum-Welch algorithm for multiple hidden markov chains |

EBHMMNBMultiEM_2chain | Run EBSeqHMM model with a fixed expected FC |

EBSeqHMM-package | EBSeqHMM: A Bayesian approach for identifying gene-expression... |

EBSeqHMMTest | Identify DE genes and classify them into their most likely... |

EBTest_ext | Extented EBTest function |

f0 | Calculate the prior predictive distribution of the... |

GeneExampleData | Simulated gene level data set with 5 ordered conditions |

GetAllPaths | Obtain all possible gene paths for an RNA-seq experiments... |

GetConfidentCalls | Obtain confident gene calls for classifying genes into... |

GetDECalls | Obtain DE gene/isoform list at a certain FDR |

IsoExampleList | Simulated isoform level data set with 5 ordered conditions |

LikefunNBHMM | Likelihood function of the Beta-Negative Binomial HMM Model |

PlotExp | Plot expression of a single gene |

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