Package: seqPattern 1.37.0
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:
seqPattern_1.37.0.tar.gz
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seqPattern_1.37.0.tgz(r-4.4-any)seqPattern_1.37.0.tgz(r-4.3-any)
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seqPattern.pdf |seqPattern.html✨
seqPattern/json (API)
NEWS
# Install 'seqPattern' in R: |
install.packages('seqPattern', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- TBPpwm - Position-weight matrix for TATA-box binding protein motif
- zebrafishPromoters - Zebrafish promoters sequences
- zebrafishPromoters24h - Zebrafish promoters genomic coordinates
On BioConductor:seqPattern-1.37.0(bioc 3.20)seqPattern-1.36.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:03617d65ea
Exports:getPatternOccurrenceListmotifScanHitsmotifScanScoresplotMotifDensityMapplotMotifOccurrenceAverageplotMotifScanScoresplotPatternDensityMapplotPatternOccurrenceAverage
Dependencies:askpassBiocGenericsBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonliteKernSmoothmimeopensslplotrixR6S4VectorssysUCSC.utilsXVectorzlibbioc
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 |