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| motifcounter-package | TFBSs analysis in DNA sequences |
| .Background | Background class definition |
| .Overlap | Overlap class definition |
| 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 |
| motifcounter | TFBSs analysis in DNA sequences |
| motifcounterOptions | Set parameters for the enrichment analysis |
| 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 |