# Set of tools to identify periodic occurrences of k-mers in DNA sequences

## Documentation for package ‘periodicDNA’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
getPeriodicity | A function to compute k-mer periodicity in sequence(s).
getPeriodicity.DNAString | A function to compute k-mer periodicity in sequence(s).
getPeriodicity.DNAStringSet | A function to compute k-mer periodicity in sequence(s).
getPeriodicity.GRanges | A function to compute k-mer periodicity in sequence(s).
getPeriodicityTrack | Function to generate a k-mer periodicity track
getPeriodicityWithIterations | A function to compute PSDs with iterations
getPeriodicityWithIterations.DNAStringSet | A function to compute PSDs with iterations
getPeriodicityWithIterations.GRanges | A function to compute PSDs with iterations
plotAggregateCoverage | A function to plot aggregated signals over sets of GRanges
plotAggregateCoverage.CompressedRleList | A function to plot aggregated signals over sets of GRanges
plotAggregateCoverage.list | A function to plot aggregated signals over sets of GRanges
plotAggregateCoverage.SimpleRleList | A function to plot aggregated signals over sets of GRanges
plotPeriodicityResults | Plot the output of getPeriodicity()
setUpBPPARAM | setUpBPPARAM
theme_ggplot2 | Personal ggplot2 theming function, adapted from roboto-condensed at https://github.com/hrbrmstr/hrbrthemes/