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[![DOI]([DOI]10.12688/f1000research.51143.1-g.svg)]( [![DOI]([DOI]10.1101/gr.265934.120-green.svg)]( [![](]( [![](]( [![](]( [![](]( [![Codecov test coverage](]( [![R-CMD-check](]( # periodicDNA <img src="man/figures/logo.png" align="right" alt="" /> ![]( ![]( ## Introduction 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). It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit [MEME]( website. ## Installation periodicDNA is available in Bioconductor. To install the current release use: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("periodicDNA") ``` For advanced users, the most recent periodicDNA can be installed from Github as follows (might be buggy): ```r install.packages("devtools") devtools::install_github("js2264/periodicDNA") library(periodicDNA) ``` ## Citation If you are using periodicDNA in your research, please cite: > [periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA]( > **J. Serizay** & J. Ahringer > F1000Research, 2021 > [Distinctive regulatory architectures of germline-active and somatic genes in C. elegans]( > **J. Serizay**, Y. Dong, J. Jänes, M. Chesney, C. Cerrato & J. Ahringer > Genome Research, 2020 ## How to use periodicDNA periodicDNA includes a vignette where its usage is illustrated. To access the vignette, please use: ```r vignette('periodicDNA') ``` ## Main functions The two main user-level functions of periodicDNA are `getPeriodicity()` and `getPeriodicityTrack()`. * `getPeriodicity()` is used to compute the power spectral density (PSD) of a chosen k-mer (i.e. `TT`) in a set of sequences. The PSD score at a given period indicates the strength of the k-mer at this period. * `getPeriodicityTrack()` can be used to generate linear tracks representing the periodicity strength of a given k-mer at a chosen period, over genomic loci of interest. ### `getPeriodicity()` function ```r data(ce11_TSSs) PSDs <- getPeriodicity( ce11_TSSs[['Ubiq.']], genome = 'BSgenome.Celegans.UCSC.ce11', motif = 'TT', BPPARAM = MulticoreParam(12), n_shuffling = 100 ) plotPeriodicityResults(PSDs) ``` ### `getPeriodicityTrack()` function ```r data(ce11_proms) WW_10bp <- getPeriodicityTrack( genome = 'BSgenome.Celegans.UCSC.ce11', granges = ce11_proms, motif = 'WW', period = 10, bw_file = '', BPPARAM = MulticoreParam(12) ) ``` **Warning**: It is recommended to run this command across many processors using BiocParallel. This command typically takes one day to produce a periodicity track over 15,000 GRanges of 150 bp (with default parameters) using `BPPARAM = MulticoreParam(12)`. It is highly recommended to run this command in a new `screen` session. ## Contributions Code contributions, bug reports, fixes and feature requests are most welcome. Please make any pull requests against the master branch at and file issues at ## License **periodicDNA** is licensed under the GPL-3 license.