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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("seqPattern")
AuthorVanja Haberle <vanja.haberle@gmail.com>
Bioconductor views SequenceMatching Visualization
Date of publicationNone
MaintainerVanja Haberle <vanja.haberle@gmail.com>
LicenseGPL-3
Version1.8.0

View on Bioconductor

Functions

getPatternOccurrenceList Man page
getPatternOccurrenceList,DNAStringSet-method Man page
motifScanHits Man page
motifScanHits,DNAStringSet,matrix-method Man page
motifScanScores Man page
motifScanScores,DNAStringSet,matrix-method Man page
plotMotifDensityMap Man page
plotMotifDensityMap,DNAStringSet,matrix-method Man page
plotMotifOccurrenceAverage Man page
plotMotifOccurrenceAverage,DNAStringSet,matrix-method Man page
plotMotifScanScores Man page
plotMotifScanScores,DNAStringSet,matrix-method Man page
plotPatternDensityMap Man page
plotPatternDensityMap,DNAStringSet-method Man page
plotPatternOccurrenceAverage Man page
plotPatternOccurrenceAverage,DNAStringSet-method Man page
seqPattern Man page
seqPattern-package Man page
TBPpwm Man page
zebrafishPromoters Man page
zebrafishPromoters24h Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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