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| seqPattern-package | Visualising oligonucleotide patterns and motif occurences across a set of ordered sequences |
| getPatternOccurrenceList | Occurrence of sequence patterns in a set of ordered sequences |
| getPatternOccurrenceList-method | Occurrence of sequence patterns in a set of ordered sequences |
| motifScanHits | Occurrence of motifs in a set of ordered sequences |
| motifScanHits-method | Occurrence of motifs in a set of ordered sequences |
| motifScanScores | Motif scanning scores for a set of ordered sequences |
| motifScanScores-method | Motif scanning scores for a set of ordered sequences |
| plotMotifDensityMap | Plotting density maps of motif occurrence |
| plotMotifDensityMap-method | Plotting density maps of motif occurrence |
| plotMotifOccurrenceAverage | Plotting average profile of motif occurrence |
| plotMotifOccurrenceAverage-method | Plotting average profile of motif occurrence |
| plotMotifScanScores | Plotting heatmap of motif scanning scores |
| plotMotifScanScores-method | Plotting heatmap of motif scanning scores |
| plotPatternDensityMap | Plotting density maps of sequence pattern occurrence |
| plotPatternDensityMap-method | Plotting density maps of sequence pattern occurrence |
| plotPatternOccurrenceAverage | Plotting average profile of sequence pattern occurrence |
| plotPatternOccurrenceAverage-method | Plotting average profile of sequence pattern occurrence |
| seqPattern | Visualising oligonucleotide patterns and motif occurences across a set of ordered sequences |
| TBPpwm | Position-weight matrix for TATA-box binding protein motif |
| zebrafishPromoters | Zebrafish promoters sequences |
| zebrafishPromoters24h | Zebrafish promoters genomic coordinates |