Package: seqPattern 1.39.0
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_1.39.0.tar.gz
seqPattern_1.39.0.zip(r-4.5)seqPattern_1.39.0.zip(r-4.4)seqPattern_1.39.0.zip(r-4.3)
seqPattern_1.39.0.tgz(r-4.4-any)seqPattern_1.39.0.tgz(r-4.3-any)
seqPattern_1.39.0.tar.gz(r-4.5-noble)seqPattern_1.39.0.tar.gz(r-4.4-noble)
seqPattern_1.39.0.tgz(r-4.4-emscripten)seqPattern_1.39.0.tgz(r-4.3-emscripten)
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-1.39.0(bioc 3.21)seqPattern-1.38.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 23 days agofrom:f37ec96cd4. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
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 |