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 | "psam" methods |
$<--method | "motifSig" methods |
$<--method | Class 'ouNode' |
$<--method | "pcm" methods |
$<--method | "pfm" methods |
$<--method | "psam" methods |
addBlank | "pfm" methods |
addBlank-method | "pcm" methods |
addBlank-method | "pfm" methods |
addBlank-method | "psam" methods |
browseMotifs | browse motifs |
browseMotifs-shiny | Shiny bindings for browseMotifs |
browseMotifsOutput | Shiny bindings for browseMotifs |
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 |
importMatrix | import motifs from local files |
matrixReverseComplement | "pfm" methods |
matrixReverseComplement-method | "pcm" methods |
matrixReverseComplement-method | "pfm" methods |
matrixReverseComplement-method | "psam" 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 |
plot-method | "psam" methods |
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 | "psam" methods |
psam-class | Class '"psam"' |
readPCM | read pcm from a path |
renderbrowseMotifs | Shiny bindings for browseMotifs |
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 |