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

Package index
Search the jianhong/motifStack package
Vignettes
Functions
233
Source code
36
Man pages
53
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jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
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API

API for jianhong/motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

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
jianhong/motifStack documentation built on Nov. 5, 2024, 7:47 a.m.

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