R package for analysing TFBSs in DNA sequences

Background-class | Background class definition |

clumpSizeDist | Clump size distribution |

combinatorialDist | Combinatrial model approximation of the number of motif hits |

compoundPoissonDist | Compound Poisson Approximation |

computeClumpStartProb | Computes the Clump start probability based on a Markov model |

generateDNAString | Generate DNAString |

generateDNAStringSet | Generate DNAStringSet |

getAlpha | Accessor to slot alpha |

getBeta | Accessor to slot beta |

getBeta3p | Accessor to slot beta3p |

getBeta5p | Accessor to slot beta |

getCounts | Accessor to slot counts |

getGamma | Accessor to slot gamma |

getOrder | Accessor to slot order |

getSinglestranded | Accessor to slot singlestranded |

getStation | Accessor to slot station |

getTrans | Accessor to slot trans |

lenSequences | Length of sequences in a given fasta file |

markovModel | Markov model for generating Y_1Y_2_Y3 ... |

motifAndBackgroundValid | Check valididity of PFM with background |

motifcounterOptions | Set parameters for the enrichment analysis |

motifcounter-package | TFBSs analysis in DNA sequences |

motifEnrichment | Enrichment of motif hits |

motifHitProfile | Motif hit profile across multiple sequences |

motifHits | Motif hit observations |

motifValid | Check valididity of PFM |

normalizeMotif | Normalizes a PFM |

numMotifHits | Number of motif hits in a set of DNA sequences |

Overlap-class | Overlap class definition |

probOverlapHit | Overlapping motif hit probabilities |

readBackground | Estimates a background model from a set of DNA sequences |

revcompMotif | Reverse complements a PFM |

scoreDist | Score distribution |

scoreDistBf | Score distribution |

scoreDistEmpirical | Empirical score distribution |

scoreHistogram | Score histogram |

scoreHistogramSingleSeq | Score histogram on a single sequence |

scoreProfile | Score profile across multiple sequences |

scoreSequence | Score observations |

scoreStrand | Score strand |

scoreThreshold | Score threshold |

sigLevel | Retrieve the false positive probability |

simulateClumpSizeDist | Empirical clump size distribution |

simulateNumHitsDist | Empirical number of motif hits distribution |

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