Global functions | |
---|---|
$,marker-method | Man page |
$,motifSig-method | Man page |
$,ouNode-method | Man page |
$,pcm-method | Man page |
$,pfm-method | Man page |
$,psam-method | Man page |
$,pssm-method | Man page |
$<-,marker-method | Man page |
$<-,motifSig-method | Man page |
$<-,ouNode-method | Man page |
$<-,pcm-method | Man page |
$<-,pfm-method | Man page |
$<-,psam-method | Man page |
$<-,pssm-method | Man page |
AAmotifAlignment | Man page Source code |
DNAmotifAlignment | Man page Source code |
DNAmotifToRNAmotif | Man page Source code |
Eval2Pval | Source code |
GeomMotif | Man page |
SWU | Source code |
UngappedAlignment | Source code |
UngappedAlignmentAA | Source code |
UngappedPCCAlignment | Source code |
addBlank | Man page |
addBlank,pcm,numeric,logical-method | Man page |
addBlank,pfm,numeric,logical-method | Man page |
addBlank,psam,numeric,logical-method | Man page |
addBlank,pssm,numeric,logical-method | Man page |
addPseudolog2 | Source code |
alignmentByPCC | Source code |
as | Man page |
as() | Man page |
as.data.frame,pcm-method | Man page |
as.data.frame,pfm-method | Man page |
as.data.frame,psam-method | Man page |
as.data.frame,pssm-method | Man page |
browseMotifs | Man page Source code |
browseMotifs-shiny | Man page |
browseMotifsOutput | Man page Source code |
calF | Man page Source code |
calI | Man page Source code |
checkALLR | Source code |
checkInteger | Source code |
checkSummary | Source code |
clusterMotifs | Man page Source code |
coerce | Man page |
coerce() | Man page |
coerce,pcm,matrix-method | Man page |
coerce,pfm,matrix-method | Man page |
coerce,psam,matrix-method | Man page |
coerce,pssm,matrix-method | Man page |
colalpha | Source code |
coloredSymbols | Source code |
colorset | Man page Source code |
compare2profiles | Man page Source code |
compareProfiles | Man page Source code |
condenseByGroup | Source code |
dpGlobal | Man page Source code |
dpLocal | Man page Source code |
format,pcm-method | Man page |
format,pfm-method | Man page |
format,psam-method | Man page |
format,pssm-method | Man page |
frequence | Man page |
frequence,motifSig-method | Man page |
geom_motif | Man page Source code |
getALLRbyBase | Source code |
getALLRscoreFromCounts | Man page Source code |
getAlignedICWithoutGap | Source code |
getAlignedPCCWithoutGap | Source code |
getDistance | Man page Source code |
getEval | Source code |
getHomoDimerCenter | Source code |
getIC | Man page |
getIC,matrix,matrix-method | Man page |
getIC,matrix,numeric-method | Man page |
getIC,pcm,ANY-method | Man page |
getIC,pfm,ANY-method | Man page |
getICbyBase | Source code |
getIE | Source code |
getPFMid | Source code |
getParentNode | Source code |
getRankedUniqueMotifs | Man page Source code |
getScore | Man page Source code |
getoffsetPosByIC | Source code |
getoffsetPosByIC_old | Source code |
getoffsetPosByPCC | Source code |
grid.eti | Source code |
hex2psrgb | Source code |
highlightCol | Man page |
importCisBP | Source code |
importFASTAlikeFile | Source code |
importM_beeml | Source code |
importM_cisbp | Source code |
importM_cm | Source code |
importM_jaspar | Source code |
importM_meme | Source code |
importM_pcm | Source code |
importM_pfm | Source code |
importM_psam | Source code |
importM_scpd | Source code |
importM_transfac | Source code |
importM_xmatrix | Source code |
importMatrix | Man page Source code |
importMulCisBP | Source code |
importMulFASTAlike | Source code |
importMulTRANSFAClike | Source code |
importSVG | Source code |
importTRANSFAClikeFile | Source code |
isHomoDimer | Source code |
makeLeaveNames | Source code |
marker | Man page |
marker-class | Man page |
matalign | Man page Source code |
matalignOut2dist | Source code |
matrixReverseComplement | Man page |
matrixReverseComplement,pcm-method | Man page |
matrixReverseComplement,pfm-method | Man page |
matrixReverseComplement,psam-method | Man page |
matrixReverseComplement,pssm-method | Man page |
mergeMotifs | Man page Source code |
motifCircos | Man page |
motifCloud | Man page Source code |
motifGrob | Man page Source code |
motifHclust | Man page Source code |
motifPiles | Man page |
motifSig | Man page |
motifSig-class | Man page |
motifSignature | Man page Source code |
motifStack | Man page Source code |
motifStack-package | Man page |
nodelist | Man page |
nodelist,motifSig-method | Man page |
ouNode | Man page |
ouNode-class | Man page |
pcm | Man page |
pcm-class | Man page |
pcm2pfm | Man page |
pcm2pfm,data.frame,ANY-method | Man page |
pcm2pfm,data.frame,numeric-method | Man page |
pcm2pfm,list,ANY-method | Man page |
pcm2pfm,list,numeric-method | Man page |
pcm2pfm,matrix,ANY-method | Man page |
pcm2pfm,matrix,numeric-method | Man page |
pcm2pfm,pcm,ANY-method | Man page |
pcm2pssm | Man page |
pcm2pssm,data.frame,ANY-method | Man page |
pcm2pssm,data.frame,numeric-method | Man page |
pcm2pssm,list,ANY-method | Man page |
pcm2pssm,list,numeric-method | Man page |
pcm2pssm,matrix,ANY-method | Man page |
pcm2pssm,matrix,numeric-method | Man page |
pcm2pssm,pcm,ANY-method | Man page |
pfm | Man page |
pfm-class | Man page |
pfm2pcm | Source code |
pfm2pwm | Man page Source code |
pfmList2matrixList | Source code |
plot | Man page |
plot,pcm,ANY-method | Man page |
plot,pfm,ANY-method | Man page |
plot,psam,ANY-method | Man page |
plot,pssm,ANY-method | Man page |
plotAffinityLogo | Man page Source code |
plotMarkers | Source code |
plotMotifLogo | Man page Source code |
plotMotifLogoA | Man page Source code |
plotMotifLogoStack | Man page Source code |
plotMotifLogoStackWithTree | Man page Source code |
plotMotifOverMotif | Man page Source code |
plotMotifStackWithPhylog | Man page Source code |
plotMotifStackWithRadialPhylog | Man page |
plotXaxis | Man page Source code |
plotYaxis | Man page Source code |
psam | Man page |
psam-class | Man page |
pssm | Man page |
pssm-class | Man page |
readPCM | Man page Source code |
readPWM | Source code |
renderbrowseMotifs | Man page Source code |
reorderUPGMAtree | Man page Source code |
sigColor | Man page |
sigColor,motifSig-method | Man page |
signatures | Man page |
signatures,motifSig-method | Man page |
traceBackGlobal | Man page Source code |
traceBackLocal | Man page Source code |
trimMotif | Man page |
trimMotif,pcm,numeric-method | Man page |
trimMotif,pfm,numeric-method | Man page |
ungappedScore | Source code |
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