Differential Expression Analysis of RNA-seq Data with Integrated Likelihood Method

condition | The conditions of Mont&pick data |

count.data | The count table of Montgomery and Pickrell data. |

edgeR.QL.running | Implement Quasi likelihood method by default settings. |

Hessian | Hessian matrix with respect to the dispersion. |

intSEQ | Implement integrated likelihood ratio test. |

intSEQ-package | Differential Analysis of RNA-seq Data with Integrated... |

joint.like | Calculate the joint likelihood |

joint.likelihood | Calculate the joint likelihood of a vector of dispersion. |

likelihoodpercond | The likelihood in each group. |

limma.trans.running | Transformation method with limma. |

limma.voom.running | Implement voom with limma by default settings. |

marginal.LR | Calculate the integrated likelihood ratio. |

mednorm | Median normalization method for limma trans. |

NBsimu | Generate synthetic RNA-seq data. |

pcut | Calculate the proportion of rejections for given levels. |

plotComp | Plot the simulation comparison results. |

ran.nb | Generate negative binomial random samples. |

ran.poi | Generate Poisson random sample. |

sample.nb | Generate negative binomial count table random sample. |

show | Show the result of 'intSEQ' |

simuComp | Simulation for the four methods and compare the p value. |

summary | Summary of comparison results. |

tran1 | The transformation function of limma.trans. |

tran.est | Estimate the coefficient in limma trans. |

tran.reg | The regression part of limma trans. |

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