Differential gene expression analysis based on the negative binomial distribution

adjustScvForBias | Adjust an SCV value for the bias arising when it is... |

conditions | Accessor functions for the 'conditions' information in a... |

CountDataSet-class | Class "CountDataSet" - a container for count data from HTS... |

counts | Accessors for the 'counts' slot of a CountDataSet object. |

dispTable | Accessor function for the dispTable information in a... |

estimateDispersions | Estimate and fit dispersions for a CountDataSet. |

estimateSizeFactors | Estimate the size factors for a CountDataSet |

estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust... |

estimateVarianceFunctions | REMOVED |

fitInfo | Accessor function for the fitInfo objects in a CountDataSet |

fitNbinomGLMs | Fit a generalized linear model (GLM) for each gene. |

fitNbinomGLMsForMatrix | Fit negative binomial GLMs to a count matrix. |

getBaseMeansAndVariances | Perform row-wise estimates of base-level means and variances... |

getVarianceStabilizedData | Apply a variance stabilizing transformation (VST) to the... |

makeExampleCountDataSet | make a simple example CountDataSet with random data |

nbinomGLMTest | Perform chi-squared tests comparing two sets of GLM fits |

nbinomTest | Test for differences between the base means for two... |

nbinomTestForMatrices | Perform row-wise tests for differences between the base means... |

nbkd.sf | GLM family for a negative binomial with known dispersion and... |

newCountDataSet | Create a CountDataSet object |

newCountDataSetFromHTSeqCount | Create a new CountDataSet from count files generated with... |

plotDispEsts | Plot dispersion estimates and fitted values |

plotMA | Makes a so-called "MA-plot" |

plotPCA | Sample PCA plot from variance-stabilized data |

residualsEcdfPlot | REMOVED |

scvPlot | REMOVED |

sizeFactors | Accessor functions for the 'sizeFactors' information in a... |

varianceFitDiagnostics | REMOVED |

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