Empirical Bayesian analysis of patterns of differential expression in count data

allModels | Function to generate all possible models for a countData... |

baySeq-classes | baySeq - classes |

baySeq-package | Empirical Bayesian analysis of patterns of differential... |

bimodalSep | A function that, given a numeric vector, finds the value... |

CDPost | 'countData' object derived from data file 'simData' with... |

CDPriors | 'countData' object derived from data file 'simData' with... |

densityFunction | Class '"densityFunction"' |

densityFunctions | Lists all currently available densityFunctions. |

getLibsizes | Estimates library scaling factors (library sizes) for count... |

getLikelihoods | Finds posterior likelihoods for each count or paired count as... |

getPosteriors | An internal function in the baySeq package for calculating... |

getPriors | Estimates prior parameters for the underlying distributions... |

getTPs | Gets the number of true positives in the top n counts... |

makeOrderings | Construct orderings for count data given a model structure... |

marginaliseEqual | Computes marginal likelihoods that two replicate groups are... |

marginalisePairwise | Computes marginal likelihoods that two replicate groups... |

methObservables | Generation of intermediate values in likelihood estimation... |

mobAnnotation | Annotation data for a set of small RNA loci derived from... |

mobData | Data from a set of small RNA sequencing experiments carried... |

pairData | Simulated data for testing the baySeq package methods for... |

plotMA.CD | 'MA'-plot for count data. |

plotNullPrior | Plots distribution of null function and shows the threshold... |

plotPosteriors | Plots the posterior likelihoods estimated for a 'countData'... |

plotPriors | Plots the density of the log values estimated for the mean... |

selectTop | Selects the top genomic events, based on posterior... |

simData | Simulated data for testing the baySeq package methods |

summarisePosteriors | Summarises expected number of genomic events given the... |

topCounts | Get the top counts corresponding to some group from a... |

zimData | Simulated data for testing the baySeq package methods |

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