DNAmotifAlignment       align DNA motifs
colorset                retrieve color setting for logo
getRankedUniqueMotifs   get the unique motif in each category grouped
                        by distance
highlightCol            add alpha transparency value to a color
motifCircos             plot sequence logo stacks with a radial
                        phylogenic tree and multiple color rings
motifCloud              plot a DNA sequence logo cloud
motifPiles              plot sequence logo stacks with a linear
                        phylogenic tree and multiple color sets
motifSig                "motifSig" methods
motifSig-class          Class '"motifSig"'
motifSignature          get signatures from motifs
motifStack              plot a DNA sequence logo stack
motifStack-package      Plot stacked logos for single or multiple DNA,
                        RNA and amino acid sequence
ouNode-class            Class 'ouNode'
pcm                     "pcm" methods
pcm-class               Class '"pcm"'
pfm                     "pfm" methods
pfm-class               Class '"pfm"'
pfm2pwm                 convert pfm object to PWM
plotMotifLogo           plot sequence logo
plotMotifLogoA          plot sequence logo without plot.new
plotMotifLogoStack      plot sequence logos stack
plotMotifLogoStackWithTree
                        plot sequence logos stack with hierarchical
                        cluster tree
plotMotifStackWithPhylog
                        plot sequence logo stacks with a ape4-style
                        phylogenic tree
plotMotifStackWithRadialPhylog
                        plot sequence logo stacks with a radial
                        phylogenic tree
plotXaxis               plot x-axis
plotYaxis               plot y-axis
readPCM                 read pcm from a path
