Plot stacked logos for single or multiple DNA, RNA and amino acid sequence


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Documentation for package ‘motifStack’ version 1.10.2

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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
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