A biophysical model for transcription factor binding affinities

affinity | compute transcription factor binding site affinity |

evaluate.ranking | Evaluate Ranking |

exactgevparams | Precalculated generalized extreme value distribution... |

fit.gev | Fit a gev distribution for a pwm matrix. |

get.affinity.cutoff | determine significance threshold for tRap affinities |

gevparams | parameters for the fitted extreme value distributions for... |

jaspar | The JASPAR transcription factor database in the format... |

local.paffinity | Calculate local p-values |

normalize.pwm | normalize a PWM |

paffinity | compute p-values for affinity values |

R_affinity_multi | Calculate the TRAP affinity for each position along one or... |

R_affinity_sum_multi | Calculate the TRAP affinity for one or more sequences (one... |

rank.factors | Rank transcription factors according to changes in binding... |

read.jaspar | read a jaspar matrix |

read.pscm | read a PSCM |

read.transfac | read a transfac matrix |

read.transfac.dir | read a directory of transfac matrices |

scan.sequence | identify TFBS hits in the sequence(s) |

tRap-package | compute transcription factor binding site affinity |

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