# Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences

## Documentation for package ‘seqPattern’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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