A B C D F G H I M N O P R S T misc
motifStack-package | Plot stacked logos for single or multiple DNA, RNA and amino acid sequence |
AAmotifAlignment | align AA motifs |
addBlank | Class '"pcm"' |
addBlank-method | Class '"pcm"' |
addBlank-method | Class '"pfm"' |
addBlank-method | Class '"psam"' |
addBlank-method | Class '"pssm"' |
as | Class '"pcm"' |
as() | Class '"psam"' |
as.data.frame-method | Class '"pcm"' |
as.data.frame-method | Class '"pfm"' |
as.data.frame-method | Class '"psam"' |
as.data.frame-method | Class '"pssm"' |
browseMotifs | browse motifs |
browseMotifs-shiny | Shiny bindings for browseMotifs |
browseMotifsOutput | Shiny bindings for browseMotifs |
calF | calculate frequence |
calI | calculate I' |
clusterMotifs | cluster motifs |
coerce | Class '"pfm"' |
coerce() | Class '"pssm"' |
coerce-method | Class '"pcm"' |
coerce-method | Class '"pfm"' |
coerce-method | Class '"psam"' |
coerce-method | Class '"pssm"' |
colorset | retrieve color setting for logo |
compare2profiles | compare two profiles |
compareProfiles | comapre w pcm |
DNAmotifAlignment | align DNA motifs |
DNAmotifToRNAmotif | convert DNA motif into RNA motif |
dpGlobal | Global alignment version |
dpLocal | Dynamic programming function, local version |
format-method | Class '"pcm"' |
format-method | Class '"pfm"' |
format-method | Class '"psam"' |
format-method | Class '"pssm"' |
frequence | Class '"motifSig"' |
frequence-method | Class '"motifSig"' |
GeomMotif | GeomMotif object |
geom_motif | geom_motif |
getALLRscoreFromCounts | calculate ALLR from counts |
getDistance | Calculate distances between two profiles |
getIC | Class '"pcm"' |
getIC-method | Class '"pcm"' |
getIC-method | Class '"pfm"' |
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 'marker' |
marker-class | Class 'marker' |
matalign | Matrix Aligner |
matrixReverseComplement | Class '"pcm"' |
matrixReverseComplement-method | Class '"pcm"' |
matrixReverseComplement-method | Class '"pfm"' |
matrixReverseComplement-method | Class '"psam"' |
matrixReverseComplement-method | Class '"pssm"' |
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 '"motifSig"' |
motifSig-class | Class '"motifSig"' |
motifSignature | get signatures from motifs |
motifStack | plot a DNA sequence logo stack |
nodelist | Class '"motifSig"' |
nodelist-method | Class '"motifSig"' |
ouNode | Class 'ouNode' |
ouNode-class | Class 'ouNode' |
pcm | Class '"pcm"' |
pcm-class | Class '"pcm"' |
pcm2pfm | Class '"pcm"' |
pcm2pfm-method | Class '"pcm"' |
pcm2pssm | Class '"pcm"' |
pcm2pssm-method | Class '"pcm"' |
pfm | Class '"pfm"' |
pfm-class | Class '"pfm"' |
pfm2pwm | convert pfm object to PWM |
plot | Class '"pcm"' |
plot-method | Class '"pcm"' |
plot-method | Class '"pfm"' |
plot-method | Class '"psam"' |
plot-method | Class '"pssm"' |
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 '"psam"' |
psam-class | Class '"psam"' |
pssm | Class '"pssm"' |
pssm-class | Class '"pssm"' |
readPCM | read pcm from a path |
renderbrowseMotifs | Shiny bindings for browseMotifs |
reorderUPGMAtree | re-order UPGMA tree |
sigColor | Class '"motifSig"' |
sigColor-method | Class '"motifSig"' |
signatures | Class '"motifSig"' |
signatures-method | Class '"motifSig"' |
traceBackGlobal | traceback global |
traceBackLocal | traceback local |
trimMotif | Class '"pcm"' |
trimMotif-method | Class '"pcm"' |
trimMotif-method | Class '"pfm"' |
$-method | Class 'marker' |
$-method | Class '"motifSig"' |
$-method | Class 'ouNode' |
$-method | Class '"pcm"' |
$-method | Class '"pfm"' |
$-method | Class '"psam"' |
$-method | Class '"pssm"' |
$<--method | Class 'marker' |
$<--method | Class '"motifSig"' |
$<--method | Class 'ouNode' |
$<--method | Class '"pcm"' |
$<--method | Class '"pfm"' |
$<--method | Class '"psam"' |
$<--method | Class '"pssm"' |
_PACKAGE | Plot stacked logos for single or multiple DNA, RNA and amino acid sequence |