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| motifStack-package | Plot stacked logos for single or multiple DNA, RNA and amino acid sequence |
| $-method | "motifSig" methods |
| $-method | Class 'ouNode' |
| $-method | "pcm" methods |
| $-method | "pfm" methods |
| $<--method | "motifSig" methods |
| $<--method | Class 'ouNode' |
| $<--method | "pcm" methods |
| $<--method | "pfm" methods |
| addBlank | "pfm" methods |
| addBlank-method | "pcm" methods |
| addBlank-method | "pfm" methods |
| colorset | retrieve color setting for logo |
| DNAmotifAlignment | align DNA motifs |
| frequence | "motifSig" methods |
| frequence-method | "motifSig" methods |
| getIC | "pfm" methods |
| getIC-method | "pcm" methods |
| getIC-method | "pfm" methods |
| getRankedUniqueMotifs | get the unique motif in each category grouped by distance |
| highlightCol | add alpha transparency value to a color |
| matrixReverseComplement | "pfm" methods |
| matrixReverseComplement-method | "pcm" methods |
| matrixReverseComplement-method | "pfm" methods |
| 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 |
| 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 |
| nodelist | "motifSig" methods |
| nodelist-method | "motifSig" methods |
| ouNode | Class 'ouNode' |
| ouNode-class | Class 'ouNode' |
| pcm | "pcm" methods |
| pcm-class | Class '"pcm"' |
| pcm2pfm | "pcm" methods |
| pcm2pfm-method | "pcm" methods |
| pfm | "pfm" methods |
| pfm-class | Class '"pfm"' |
| pfm2pwm | convert pfm object to PWM |
| plot-method | "pcm" methods |
| plot-method | "pfm" methods |
| 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 |
| readPCM | read pcm from a path |
| reorderUPGMAtree | re-order UPGMA tree |
| sigColor | "motifSig" methods |
| sigColor-method | "motifSig" methods |
| signatures | "motifSig" methods |
| signatures-method | "motifSig" methods |
| trimMotif | "pcm" methods |
| trimMotif-method | "pcm" methods |
| trimMotif-method | "pfm" methods |