# Generated by roxygen2: do not edit by hand

export(AAmotifAlignment)
export(DNAmotifAlignment)
export(DNAmotifToRNAmotif)
export(GeomMotif)
export(browseMotifs)
export(browseMotifsOutput)
export(clusterMotifs)
export(colorset)
export(geom_motif)
export(getRankedUniqueMotifs)
export(highlightCol)
export(importMatrix)
export(matalign)
export(mergeMotifs)
export(motifCircos)
export(motifCloud)
export(motifGrob)
export(motifHclust)
export(motifPiles)
export(motifSignature)
export(motifStack)
export(pfm2pwm)
export(plotAffinityLogo)
export(plotMotifLogo)
export(plotMotifLogoA)
export(plotMotifLogoStack)
export(plotMotifLogoStackWithTree)
export(plotMotifOverMotif)
export(plotMotifStackWithPhylog)
export(plotMotifStackWithRadialPhylog)
export(readPCM)
export(renderbrowseMotifs)
export(reorderUPGMAtree)
exportClasses(marker)
exportClasses(motifSig)
exportClasses(ouNode)
exportClasses(pcm)
exportClasses(pfm)
exportClasses(psam)
exportClasses(pssm)
exportMethods(`$<-`)
exportMethods(`$`)
exportMethods(addBlank)
exportMethods(as.data.frame)
exportMethods(coerce)
exportMethods(format)
exportMethods(frequence)
exportMethods(getIC)
exportMethods(matrixReverseComplement)
exportMethods(nodelist)
exportMethods(pcm2pfm)
exportMethods(pcm2pssm)
exportMethods(plot)
exportMethods(sigColor)
exportMethods(signatures)
exportMethods(trimMotif)
import(methods)
importFrom(Biostrings,PWM)
importFrom(XML,xmlParse)
importFrom(XML,xmlToList)
importFrom(ade4,hclust2phylog)
importFrom(ade4,scatterutil.eti)
importFrom(ggplot2,Geom)
importFrom(ggplot2,aes)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,layer)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.off)
importFrom(grDevices,dev.size)
importFrom(grDevices,grey)
importFrom(grDevices,rainbow)
importFrom(grDevices,rgb)
importFrom(grDevices,svg)
importFrom(graphics,abline)
importFrom(graphics,box)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,plot.default)
importFrom(graphics,plot.new)
importFrom(graphics,plot.window)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,segments)
importFrom(graphics,strheight)
importFrom(graphics,strwidth)
importFrom(graphics,symbols)
importFrom(graphics,text)
importFrom(grid,arrow)
importFrom(grid,convertHeight)
importFrom(grid,convertUnit)
importFrom(grid,gList)
importFrom(grid,gTree)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.lines)
importFrom(grid,grid.newpage)
importFrom(grid,grid.points)
importFrom(grid,grid.polygon)
importFrom(grid,grid.rect)
importFrom(grid,grid.segments)
importFrom(grid,grid.text)
importFrom(grid,grid.xaxis)
importFrom(grid,linesGrob)
importFrom(grid,plotViewport)
importFrom(grid,pointsGrob)
importFrom(grid,polygonGrob)
importFrom(grid,popViewport)
importFrom(grid,pushViewport)
importFrom(grid,rectGrob)
importFrom(grid,segmentsGrob)
importFrom(grid,stringHeight)
importFrom(grid,stringWidth)
importFrom(grid,textGrob)
importFrom(grid,unit)
importFrom(grid,viewport)
importFrom(grid,xaxisGrob)
importFrom(grid,yaxisGrob)
importFrom(htmlwidgets,createWidget)
importFrom(htmlwidgets,shinyRenderWidget)
importFrom(htmlwidgets,shinyWidgetOutput)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,predict)
importFrom(stats,rgamma)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats4,plot)
importFrom(utils,combn)
importFrom(utils,install.packages)
importFrom(utils,read.delim)
importFrom(utils,read.table)
