seqPattern (version 1.4.0)

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

Description

Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

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Version

1.4.0

License

GPL-3

Maintainer

Vanja Haberle

Last Published

February 15th, 2017

Functions in seqPattern (1.4.0)

TBPpwm

Position-weight matrix for TATA-box binding protein motif

plotPatternDensityMap

Plotting density maps of sequence pattern occurrence

plotMotifScanScores

Plotting heatmap of motif scanning scores

zebrafishPromoters24h

Zebrafish promoters genomic coordinates

motifScanScores

Motif scanning scores for a set of ordered sequences

seqPattern-package

Visualising oligonucleotide patterns and motif occurences across a set of ordered sequences

plotPatternOccurrenceAverage

Plotting average profile of sequence pattern occurrence

motifScanHits

Occurrence of motifs in a set of ordered sequences

plotMotifDensityMap

Plotting density maps of motif occurrence

plotMotifOccurrenceAverage

Plotting average profile of motif occurrence

getPatternOccurrenceList

Occurrence of sequence patterns in a set of ordered sequences

zebrafishPromoters

Zebrafish promoters sequences