# Generated by roxygen2: do not edit by hand

export(forceReverse)
export(initialOrder)
export(methyl_average_status)
export(methyl_percent_sites)
export(methyl_proportion)
export(methylscaper)
export(plotSequence)
export(prepSC)
export(refineFunction)
export(runAlign)
export(subsetSC)
import(data.table)
import(seriation)
import(shiny)
import(shinyFiles)
importFrom(BiocParallel,bplapply)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNA_ALPHABET)
importFrom(Biostrings,reverseComplement)
importFrom(Rfast,Dist)
importFrom(SummarizedExperiment,assay)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(grDevices,cairo_pdf)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,segments)
importFrom(graphics,title)
importFrom(methods,is)
importFrom(pwalign,alignedPattern)
importFrom(pwalign,alignedSubject)
importFrom(pwalign,mismatchTable)
importFrom(pwalign,pairwiseAlignment)
importFrom(pwalign,score)
importFrom(seqinr,c2s)
importFrom(seqinr,read.fasta)
importFrom(seqinr,s2c)
importFrom(seriation,get_order)
importFrom(seriation,seriate)
importFrom(shinyjs,disabled)
importFrom(shinyjs,enable)
importFrom(shinyjs,showElement)
importFrom(shinyjs,toggleElement)
importFrom(shinyjs,useShinyjs)
importFrom(stats,as.dist)
importFrom(stats,dist)
importFrom(stats,filter)
importFrom(utils,capture.output)
importFrom(utils,data)
importFrom(utils,tail)
importFrom(utils,write.csv)
