BinQuasi |
Analyzing Replicated ChIP Sequencing Data Using Quasi-Likelihood |

BQ |
Call peaks in replicated ChIP-seq data using BinQuasi |

call.peaks |
Call peaks from a list of window-level p-values |

coef.glm |
Extract model coefficients |

count.table |
Create a matrix of ChIP-seq count data |

NBDev |
Fit a negative binomial GLM for a given design matrix |

PoisDev |
Compute Poisson deviances for a given design matrix |

QL.fit |
Fit quasi-likelihood models to replicated ChIP-seq data partitioned into a count matrix |

QL.results |
Obtain p- and q-values using results from 'QL.fit' |