Package: periodicDNA 1.17.0
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_1.17.0.tar.gz
periodicDNA_1.17.0.zip(r-4.5)periodicDNA_1.17.0.zip(r-4.4)periodicDNA_1.17.0.zip(r-4.3)
periodicDNA_1.17.0.tgz(r-4.5-any)periodicDNA_1.17.0.tgz(r-4.4-any)periodicDNA_1.17.0.tgz(r-4.3-any)
periodicDNA_1.17.0.tar.gz(r-4.5-noble)periodicDNA_1.17.0.tar.gz(r-4.4-noble)
periodicDNA_1.17.0.tgz(r-4.4-emscripten)periodicDNA_1.17.0.tgz(r-4.3-emscripten)
periodicDNA.pdf |periodicDNA.html✨
periodicDNA/json (API)
NEWS
| # 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
- ce11_ATACseq - Ce11_ATACseq
- ce11_TSSs - Ce11_TSSs
- ce11_WW_10bp - Ce11_WW_10bp
- ce11_all_REs - Ce11_all_REs
- ce11_proms - Ce11_proms
- ce11_proms_seqs - Ce11_proms_seqs
On BioConductor:periodicDNA-1.17.0(bioc 3.21)periodicDNA-1.16.0(bioc 3.20)
sequencematchingmotifdiscoverymotifannotationsequencingcoveragealignmentdataimport
Last updated 4 months agofrom:75b48a613d. Checks:1 OK, 7 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 31 2025 |
| R-4.5-win | WARNING | Jan 31 2025 |
| R-4.5-mac | WARNING | Jan 31 2025 |
| R-4.5-linux | WARNING | Jan 31 2025 |
| R-4.4-win | WARNING | Jan 31 2025 |
| R-4.4-mac | WARNING | Jan 31 2025 |
| R-4.3-win | WARNING | Jan 31 2025 |
| R-4.3-mac | WARNING | Jan 31 2025 |
Exports:getPeriodicitygetPeriodicityTrackgetPeriodicityWithIterationsplotAggregateCoverageplotPeriodicityResultssetUpBPPARAMtheme_ggplot2
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzoo
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 |
