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

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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.

Author
Vanja Haberle <vanja.haberle@gmail.com>
Date of publication
None
Maintainer
Vanja Haberle <vanja.haberle@gmail.com>
License
GPL-3
Version
1.6.0

View on Bioconductor

Man pages

getPatternOccurrenceList
Occurrence of sequence patterns in a set of ordered sequences
motifScanHits
Occurrence of motifs in a set of ordered sequences
motifScanScores
Motif scanning scores for a set of ordered sequences
plotMotifDensityMap
Plotting density maps of motif occurrence
plotMotifOccurrenceAverage
Plotting average profile of motif occurrence
plotMotifScanScores
Plotting heatmap of motif scanning scores
plotPatternDensityMap
Plotting density maps of sequence pattern occurrence
plotPatternOccurrenceAverage
Plotting average profile of sequence pattern occurrence
seqPattern-package
Visualising oligonucleotide patterns and motif occurences...
TBPpwm
Position-weight matrix for TATA-box binding protein motif
zebrafisPromoters
Zebrafish promoters sequences
zebrafisPromoters24h
Zebrafish promoters genomic coordinates

Files in this package

seqPattern/DESCRIPTION
seqPattern/NAMESPACE
seqPattern/NEWS
seqPattern/R
seqPattern/R/MotifScanningFunctions.R
seqPattern/R/MotifScanningMethods.R
seqPattern/R/PatternOccurrenceFunctions.R
seqPattern/R/PatternOccurrenceMethods.R
seqPattern/R/PlottingFunctions.R
seqPattern/R/PlottingMethods.R
seqPattern/build
seqPattern/build/vignette.rds
seqPattern/data
seqPattern/data/TBPpwm.RData
seqPattern/data/datalist
seqPattern/data/zebrafishPromoters.RData
seqPattern/data/zebrafishPromoters24h.RData
seqPattern/inst
seqPattern/inst/doc
seqPattern/inst/doc/seqPattern.R
seqPattern/inst/doc/seqPattern.Rnw
seqPattern/inst/doc/seqPattern.pdf
seqPattern/inst/unitTests
seqPattern/inst/unitTests/test_MotifScanningFunctions.R
seqPattern/inst/unitTests/test_MotifScanningMethods.R
seqPattern/inst/unitTests/test_PatternOccurrenceFunctions.R
seqPattern/inst/unitTests/test_PatternOccurrenceMethods.R
seqPattern/man
seqPattern/man/TBPpwm.Rd
seqPattern/man/getPatternOccurrenceList.Rd
seqPattern/man/motifScanHits.Rd
seqPattern/man/motifScanScores.Rd
seqPattern/man/plotMotifDensityMap.Rd
seqPattern/man/plotMotifOccurrenceAverage.Rd
seqPattern/man/plotMotifScanScores.Rd
seqPattern/man/plotPatternDensityMap.Rd
seqPattern/man/plotPatternOccurrenceAverage.Rd
seqPattern/man/seqPattern-package.Rd
seqPattern/man/zebrafisPromoters.Rd
seqPattern/man/zebrafisPromoters24h.Rd
seqPattern/tests
seqPattern/tests/runTests.R
seqPattern/vignettes
seqPattern/vignettes/images
seqPattern/vignettes/images/ColorPalettes.pdf
seqPattern/vignettes/images/ConsensusDensity.jpg
seqPattern/vignettes/images/DensitySchematic.pdf
seqPattern/vignettes/images/MetaoligonucleotideDensity.jpg
seqPattern/vignettes/images/MotifAverage.pdf
seqPattern/vignettes/images/MotifDensity.jpg
seqPattern/vignettes/images/OligonucleotideAverage.pdf
seqPattern/vignettes/images/OligonucleotideDensity.jpg
seqPattern/vignettes/seqPattern.Rnw
seqPattern/vignettes/seqPattern.bib