Package: periodicDNA 1.15.0

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:Jacques Serizay [aut, cre]

periodicDNA_1.15.0.tar.gz
periodicDNA_1.15.0.zip(r-4.5)periodicDNA_1.15.0.zip(r-4.4)periodicDNA_1.15.0.zip(r-4.3)
periodicDNA_1.15.0.tgz(r-4.4-any)periodicDNA_1.15.0.tgz(r-4.3-any)
periodicDNA_1.15.0.tar.gz(r-4.5-noble)periodicDNA_1.15.0.tar.gz(r-4.4-noble)
periodicDNA_1.15.0.tgz(r-4.4-emscripten)periodicDNA_1.15.0.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

Datasets:

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-1.15.0(bioc 3.20)periodicDNA-1.14.0(bioc 3.19)

bioconductor-package

7 exports 0.61 score 77 dependencies

Last updated 2 months agofrom:cf66ae595b

Exports:getPeriodicity getPeriodicityTrack getPeriodicityWithIterations plotAggregateCoverage plotPeriodicityResults setUpBPPARAM theme_ggplot2

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cli codetools colorspace cowplot cpp11 crayon curl DelayedArray fansi farver formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales snow SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc zoo

periodicDNA

Jacques Serizay

Rendered fromperiodicDNA.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2020-09-07
Started: 2020-05-04

Citation

Development and contributors

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