Introduction to periodicDNA | Internal steps of periodicDNA | Quantifying k-mer periodicity over a set of sequences | Basic usage | Repeated shuffling of input sequences | Note | Track of periodicity over a set of Genomic Ranges | Session info
Package: periodicDNA 1.23.0
Jacques Serizay
periodicDNA: Set of tools to identify periodic occurrences of k-mers in DNA sequences
This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.
Authors:
periodicDNA_1.23.0.tar.gz
periodicDNA_1.23.0.zip(r-4.7)periodicDNA_1.23.0.zip(r-4.6)periodicDNA_1.23.0.zip(r-4.5)
periodicDNA_1.23.0.tgz(r-4.6-any)periodicDNA_1.23.0.tgz(r-4.5-any)
periodicDNA_1.23.0.tar.gz(r-4.7-any)periodicDNA_1.23.0.tar.gz(r-4.6-any)
periodicDNA_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
periodicDNA/json (API)
| # Install 'periodicDNA' in R: |
| install.packages('periodicDNA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/js2264/periodicdna/issues
Datasets:
- ce11_all_REs - Ce11_all_REs
- ce11_ATACseq - Ce11_ATACseq
- ce11_proms - Ce11_proms
- ce11_proms_seqs - Ce11_proms_seqs
- ce11_TSSs - Ce11_TSSs
- ce11_WW_10bp - Ce11_WW_10bp
On BioConductor:periodicDNA-1.23.0(bioc 3.24)periodicDNA-1.22.0(bioc 3.23)
sequencematchingmotifdiscoverymotifannotationsequencingcoveragealignmentdataimport
Last updated from:e77802fa37. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 393 | ||
| linux-devel-x86_64 | WARNING | 626 | ||
| source / vignettes | OK | 522 | ||
| linux-release-x86_64 | WARNING | 559 | ||
| macos-release-arm64 | WARNING | 297 | ||
| macos-oldrel-arm64 | WARNING | 294 | ||
| windows-devel | WARNING | 489 | ||
| windows-release | WARNING | 504 | ||
| windows-oldrel | WARNING | 497 | ||
| wasm-release | OK | 375 |
Exports:getPeriodicitygetPeriodicityTrackgetPeriodicityWithIterationsplotAggregateCoverageplotPeriodicityResultssetUpBPPARAMtheme_ggplot2
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecigarilloclicodetoolscowplotcpp11crayoncurlDelayedArrayfarverformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ce11_all_REs | ce11_all_REs |
| ce11_ATACseq | ce11_ATACseq |
| ce11_proms | ce11_proms |
| ce11_proms_seqs | ce11_proms_seqs |
| ce11_TSSs | ce11_TSSs |
| ce11_WW_10bp | ce11_WW_10bp |
| A function to compute k-mer periodicity in sequence(s). | getPeriodicity getPeriodicity.DNAString getPeriodicity.DNAStringSet getPeriodicity.GRanges |
| Function to generate a k-mer periodicity track | getPeriodicityTrack |
| A function to compute PSDs with iterations | getPeriodicityWithIterations getPeriodicityWithIterations.DNAStringSet getPeriodicityWithIterations.GRanges |
| A function to plot aggregated signals over sets of GRanges | plotAggregateCoverage plotAggregateCoverage.CompressedRleList plotAggregateCoverage.list plotAggregateCoverage.SimpleRleList |
| Plot the output of getPeriodicity() | plotPeriodicityResults |
| setUpBPPARAM | setUpBPPARAM |
| Personal ggplot2 theming function, adapted from roboto-condensed at https://github.com/hrbrmstr/hrbrthemes/ | theme_ggplot2 |
