motifStack-package | Plot stacked logos for single or multiple DNA, RNA and amino acid sequence |
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 |
matrixReverseComplement | "pfm" methods |
matrixReverseComplement-method | "pcm" methods |
matrixReverseComplement-method | "pfm" methods |
motifCloud | plot a DNA sequence logo cloud |
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"' |
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 |
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 |
signatures | "motifSig" methods |
signatures-method | "motifSig" methods |
trimMotif | "pcm" methods |
trimMotif-method | "pcm" methods |
trimMotif-method | "pfm" methods |