Package: seqPattern 1.43.0

Vanja Haberle

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

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.

Authors:Vanja Haberle <[email protected]>

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seqPattern/json (API)
NEWS

# Install 'seqPattern' in R:

install.packages('seqPattern', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

TBPpwm - Position-weight matrix for TATA-box binding protein motif
zebrafishPromoters - Zebrafish promoters sequences
zebrafishPromoters24h - Zebrafish promoters genomic coordinates

On BioConductor:seqPattern-1.43.0(bioc 3.23)seqPattern-1.42.0(bioc 3.22)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualization sequencematching

4.80 score 6 packages 12 scripts 1.4k downloads 1 mentions 8 exports 11 dependencies

Last updated from:4b1e21f539. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Total time
bioc-checks	ERROR	215
linux-devel-x86_64	NOTE	277
source / vignettes	OK	344
linux-release-x86_64	NOTE	296
macos-release-arm64	NOTE	149
macos-oldrel-arm64	NOTE	174
windows-devel	NOTE	256
windows-release	NOTE	246
windows-oldrel	NOTE	231
wasm-release	OK	191

Exports:getPatternOccurrenceList motifScanHits motifScanScores plotMotifDensityMap plotMotifOccurrenceAverage plotMotifScanScores plotPatternDensityMap plotPatternOccurrenceAverage

Dependencies:BiocGenerics Biostrings crayon generics GenomicRanges IRanges KernSmooth plotrix S4Vectors Seqinfo XVector

seqPattern

Rendered fromseqPattern.Rnwusingutils::Sweaveon Nov 23 2025.

Last update: 2015-05-08
Started: 2015-01-06

Citation

Development and contributors

Readme and manuals

Help Manual

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