AAmotifAlignment        align AA motifs
DNAmotifAlignment       align DNA motifs
DNAmotifToRNAmotif      convert DNA motif into RNA motif
GeomMotif               GeomMotif object
browseMotifs            browse motifs
browseMotifs-shiny      Shiny bindings for browseMotifs
calF                    calculate frequence
calI                    calculate I'
clusterMotifs           cluster motifs
colorset                retrieve color setting for logo
compare2profiles        compare two profiles
compareProfiles         comapre w pcm
dpGlobal                Global alignment version
dpLocal                 Dynamic programming function, local version
geom_motif              geom_motif
getALLRscoreFromCounts
                        calculate ALLR from counts
getDistance             Calculate distances between two profiles
getRankedUniqueMotifs   get the unique motif in each category grouped
                        by distance
getScore                Calculate pair_wise position score
highlightCol            add alpha transparency value to a color
importMatrix            import motifs from local files
marker-class            Class 'marker'
matalign                Matrix Aligner
mergeMotifs             merge multiple motifs
motifCircos             plot sequence logo stacks with a radial
                        phylogenic tree and multiple color rings
motifCloud              plot a DNA sequence logo cloud
motifGrob               Motif Grob
motifHclust             Hierarchical Clustering motifs
motifPiles              plot sequence logo stacks with a linear
                        phylogenic tree and multiple color sets
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-class               Class '"pcm"'
pfm-class               Class '"pfm"'
pfm2pwm                 convert pfm object to PWM
plotAffinityLogo        plot affinity logo
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
plotMotifOverMotif      plot motif over another motif
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
psam-class              Class '"psam"'
pssm-class              Class '"pssm"'
readPCM                 read pcm from a path
reorderUPGMAtree        re-order UPGMA tree
traceBackGlobal         traceback global
traceBackLocal          traceback local
