1 Introduction | 2 Getting started | 3 Example data | 4 Visualising oligonucleotide and consensus sequence densities | 5 Visualising motif occurrences | 6 Getting occurrence of sequence patterns and motifs without visualisation | 7 Session Info
Package: seqPattern 1.45.0
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_1.45.0.tar.gz
seqPattern_1.45.0.zip(r-4.7)seqPattern_1.45.0.zip(r-4.6)seqPattern_1.45.0.zip(r-4.5)
seqPattern_1.45.0.tgz(r-4.6-any)seqPattern_1.45.0.tgz(r-4.5-any)
seqPattern_1.45.0.tar.gz(r-4.7-any)seqPattern_1.45.0.tar.gz(r-4.6-any)
seqPattern_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
seqPattern/json (API)
| # 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-1.45.0(bioc 3.24)seqPattern-1.44.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:84dc096f6a. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 222 | ||
| linux-devel-x86_64 | NOTE | 348 | ||
| source / vignettes | OK | 328 | ||
| linux-release-x86_64 | NOTE | 352 | ||
| macos-release-arm64 | NOTE | 170 | ||
| macos-oldrel-arm64 | NOTE | 142 | ||
| windows-devel | NOTE | 234 | ||
| windows-release | NOTE | 233 | ||
| windows-oldrel | NOTE | 219 | ||
| wasm-release | OK | 225 |
Exports:getPatternOccurrenceListmotifScanHitsmotifScanScoresplotMotifDensityMapplotMotifOccurrenceAverageplotMotifScanScoresplotPatternDensityMapplotPatternOccurrenceAverage
Dependencies:BiocGenericsBiostringscrayongenericsGenomicRangesIRangesKernSmoothplotrixS4VectorsSeqinfoXVector
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 |