as.data.frame,SitePairSet-method	SitePairSet-class
as.data.frame,SitePairSetList-method	SitePairSetList-class
as.data.frame,SiteSet-method	SiteSet-class
as.data.frame,SiteSetList-method	SiteSetList-class
as.matrix,XMatrix-method	XMatrix-class
bg	XMatrix-class
bg,XMatrix-method	XMatrix-class
bg,XMatrixList-method	XMatrixList-class
bg<-,XMatrix-method	XMatrix-class
c,SiteSet-method	SiteSet-class
c-methods	SiteSet-class
calConservation	calConservation-methods
calConservation,character,character-method	calConservation-methods
calConservation,character,missing-method	calConservation-methods
calConservation,DNAString,DNAString-method	calConservation-methods
calConservation,DNAStringSet,missing-method	calConservation-methods
calConservation-methods	calConservation-methods
colSums,XMatrix-method	XMatrix-class
consensusMatrix,MotifSet-method	MotifSet-class
deleteMatrixHavingID	deleteMatrixHavingID-methods
deleteMatrixHavingID,character-method	deleteMatrixHavingID-methods
deleteMatrixHavingID,JASPAR2014-method	deleteMatrixHavingID-methods
deleteMatrixHavingID,JASPAR2016-method	deleteMatrixHavingID-methods
deleteMatrixHavingID,SQLiteConnection-method	deleteMatrixHavingID-methods
dim,XMatrix-method	XMatrix-class
dmmEM	dmmEM-methods
dmmEM,ANY-method	dmmEM-methods
dmmEM,matrix-method	dmmEM-methods
dmmEM,PFMatrixList-method	dmmEM-methods
dmmEM-methods	dmmEM-methods
end,SiteSet-method	SiteSet-class
getEmissionProb	getEmissionProb
getEmissionProb,TFFMDetail-method	getEmissionProb
getEmissionProb,TFFMFirst-method	getEmissionProb
getMatrixByID	getMatrixByID-methods
getMatrixByID,character-method	getMatrixByID-methods
getMatrixByID,JASPAR2014-method	getMatrixByID-methods
getMatrixByID,JASPAR2016-method	getMatrixByID-methods
getMatrixByID,SQLiteConnection-method	getMatrixByID-methods
getMatrixByName	getMatrixByID-methods
getMatrixByName,character-method	getMatrixByID-methods
getMatrixByName,JASPAR2014-method	getMatrixByID-methods
getMatrixByName,JASPAR2016-method	getMatrixByID-methods
getMatrixByName,SQLiteConnection-method	getMatrixByID-methods
getMatrixSet	getMatrixSet-methods
getMatrixSet,character-method	getMatrixSet-methods
getMatrixSet,JASPAR2014-method	getMatrixSet-methods
getMatrixSet,JASPAR2016-method	getMatrixSet-methods
getMatrixSet,SQLiteConnection-method	getMatrixSet-methods
getPosProb	getPosProb
getPosProb,TFFMDetail-method	getPosProb
getPosProb,TFFMFirst-method	getPosProb
ICMatrix	XMatrix-class
ICMatrix-class	XMatrix-class
ICMatrixList	XMatrixList-class
ICMatrixList-class	XMatrixList-class
ID	XMatrix-class
ID,XMatrix-method	XMatrix-class
ID,XMatrixList-method	XMatrixList-class
ID<-,XMatrix-method	XMatrix-class
initializeJASPARDB	deleteMatrixHavingID-methods
initializeJASPARDB,character-method	deleteMatrixHavingID-methods
initializeJASPARDB,JASPAR2014-method	deleteMatrixHavingID-methods
initializeJASPARDB,JASPAR2016-method	deleteMatrixHavingID-methods
initializeJASPARDB,SQLiteConnection-method	deleteMatrixHavingID-methods
IUPAC2Matrix	IUPAC2Matrix
length,MotifSet-method	MotifSet-class
length,SitePairSet-method	SitePairSet-class
length,SiteSet-method	SiteSet-class
length,XMatrix-method	XMatrix-class
length-methods	XMatrix-class
MA0003.2	MA0004.1
MA0004.1	MA0004.1
MA0043	MA0004.1
MA0048	MA0004.1
makeFlatFileDir	makeFlatFileDir
Matrix	XMatrix-class
Matrix,XMatrix-method	XMatrix-class
Matrix,XMatrixList-method	XMatrixList-class
Matrix<-	XMatrix-class
Matrix<-,XMatrix-method	XMatrix-class
matrixClass	XMatrix-class
matrixClass,XMatrix-method	XMatrix-class
matrixClass,XMatrixList-method	XMatrixList-class
matrixClass<-,XMatrix-method	XMatrix-class
matrixType	XMatrix-class
matrixType,ICMatrix-method	XMatrix-class
matrixType,PFMatrix-method	XMatrix-class
matrixType,PWMatrix-method	XMatrix-class
matrixType,XMatrixList-method	XMatrixList-class
matrixType-methods	XMatrix-class
MotifSet	MotifSet-class
MotifSet-class	MotifSet-class
name	XMatrix-class
name,XMatrix-method	XMatrix-class
name,XMatrixList-method	XMatrixList-class
name<-,XMatrix-method	XMatrix-class
ncol,TFFMDetail-method	TFFM-class
ncol,TFFMFirst-method	TFFM-class
ncol,XMatrix-method	XMatrix-class
parseMEMEOutput	parseMEMEOutput
pattern,SiteSet-method	SiteSet-class
permuteMatrix	permuteMatrix-methods
permuteMatrix,matrix-method	permuteMatrix-methods
permuteMatrix,PFMatrix-method	permuteMatrix-methods
permuteMatrix,PFMatrixList-method	permuteMatrix-methods
permuteMatrix-methods	permuteMatrix-methods
PFMatrix	XMatrix-class
PFMatrix-class	XMatrix-class
PFMatrixList	XMatrixList-class
PFMatrixList-class	XMatrixList-class
PFMSimilarity	PFMSimilarity-methods
PFMSimilarity,matrix,character-method	PFMSimilarity-methods
PFMSimilarity,matrix,matrix-method	PFMSimilarity-methods
PFMSimilarity,matrix,PFMatrix-method	PFMSimilarity-methods
PFMSimilarity,PFMatrix,character-method	PFMSimilarity-methods
PFMSimilarity,PFMatrix,matrix-method	PFMSimilarity-methods
PFMSimilarity,PFMatrix,PFMatrix-method	PFMSimilarity-methods
PFMSimilarity,PFMatrixList,character-method	PFMSimilarity-methods
PFMSimilarity,PFMatrixList,matrix-method	PFMSimilarity-methods
PFMSimilarity,PFMatrixList,PFMatrix-method	PFMSimilarity-methods
PFMSimilarity-methods	PFMSimilarity-methods
primary,SiteSet-method	SiteSet-class
pvalues	SiteSet-class
pvalues,SiteSet-method	SiteSet-class
pvalues,SiteSetList-method	SiteSetList-class
PWMatrix	XMatrix-class
PWMatrix-class	XMatrix-class
PWMatrixList	XMatrixList-class
PWMatrixList-class	XMatrixList-class
PWMSimilarity	PWMSimilarity-methods
PWMSimilarity,matrix,matrix-method	PWMSimilarity-methods
PWMSimilarity,matrix,PWMatrix-method	PWMSimilarity-methods
PWMSimilarity,PWMatrix,matrix-method	PWMSimilarity-methods
PWMSimilarity,PWMatrix,PWMatrix-method	PWMSimilarity-methods
PWMSimilarity,PWMatrixList,matrix-method	PWMSimilarity-methods
PWMSimilarity,PWMatrixList,PWMatrix-method	PWMSimilarity-methods
PWMSimilarity,PWMatrixList,PWMatrixList-method	PWMSimilarity-methods
PWMSimilarity-methods	PWMSimilarity-methods
readJASPARMatrix	readJASPARMatrix
readXMLTFFM	readXMLTFFM
relScore	SiteSet-class
relScore,SiteSet-method	SiteSet-class
relScore,SiteSetList-method	SiteSetList-class
reverseComplement,XMatrix-method	XMatrix-class
rowSums,XMatrix-method	XMatrix-class
rPWMDmm	rPWMDmm-methods
rPWMDmm,matrix-method	rPWMDmm-methods
rPWMDmm,PFMatrix-method	rPWMDmm-methods
rPWMDmm,PFMatrixList-method	rPWMDmm-methods
rPWMDmm-methods	rPWMDmm-methods
runMEME	runMEME-methods
runMEME,character-method	runMEME-methods
runMEME,DNAStringSet-method	runMEME-methods
sampleRanges	sampleRanges
score,SiteSet-method	SiteSet-class
searchAln	searchAln-methods
searchAln,PWMatrix,Axt,missing-method	searchAln-methods
searchAln,PWMatrix,character,character-method	searchAln-methods
searchAln,PWMatrix,character,missing-method	searchAln-methods
searchAln,PWMatrix,DNAString,DNAString-method	searchAln-methods
searchAln,PWMatrix,DNAStringSet,missing-method	searchAln-methods
searchAln,PWMatrixList,character,character-method	searchAln-methods
searchAln,PWMatrixList,character,missing-method	searchAln-methods
searchAln,PWMatrixList,DNAString,DNAString-method	searchAln-methods
searchAln,PWMatrixList,DNAStringSet,missing-method	searchAln-methods
searchPairBSgenome	searchPairBSgenome-methods
searchPairBSgenome,PWMatrix-method	searchPairBSgenome-methods
searchPairBSgenome,PWMatrixList-method	searchPairBSgenome-methods
searchPairBSgenome-methods	searchPairBSgenome-methods
searchSeq	searchSeq-methods
searchSeq,PWMatrix-method	searchSeq-methods
searchSeq,PWMatrixList-method	searchSeq-methods
searchSeq-methods	searchSeq-methods
seqLogo	seqLogo
seqLogo,ICMatrix-method	seqLogo
seqLogo,TFFM-method	seqLogo
seqname,SiteSet-method	SiteSet-class
shannon.entropy	shannon.entropy
show,SiteSet-method	SiteSet-class
site1,SitePairSet-method	SitePairSet-class
site2,SitePairSet-method	SitePairSet-class
SitePairSet	SitePairSet-class
SitePairSet-class	SitePairSet-class
SitePairSetList	SitePairSetList-class
SitePairSetList-class	SitePairSetList-class
SiteSet	SiteSet-class
SiteSet-class	SiteSet-class
SiteSetList	SiteSetList-class
SiteSetList-class	SiteSetList-class
sitesource,SiteSet-method	SiteSet-class
sitesSeq	MotifSet-class
sitesSeq,MotifSet-method	MotifSet-class
start,SiteSet-method	SiteSet-class
storeMatrix	deleteMatrixHavingID-methods
storeMatrix,character,PFMatrix-method	deleteMatrixHavingID-methods
storeMatrix,character,PFMatrixList-method	deleteMatrixHavingID-methods
storeMatrix,JASPAR2014,PFMatrix-method	deleteMatrixHavingID-methods
storeMatrix,JASPAR2014,PFMatrixList-method	deleteMatrixHavingID-methods
storeMatrix,JASPAR2016,PFMatrix-method	deleteMatrixHavingID-methods
storeMatrix,JASPAR2016,PFMatrixList-method	deleteMatrixHavingID-methods
storeMatrix,SQLiteConnection,PFMatrix-method	deleteMatrixHavingID-methods
storeMatrix,SQLiteConnection,PFMatrixList-method	deleteMatrixHavingID-methods
storeMatrix-methods	deleteMatrixHavingID-methods
strand,SiteSet-method	SiteSet-class
strand,XMatrix-method	XMatrix-class
strand,XMatrixList-method	XMatrixList-class
strand<-,XMatrix-method	XMatrix-class
tags	XMatrix-class
tags,XMatrix-method	XMatrix-class
tags,XMatrixList-method	XMatrixList-class
TFBSTools	TFBSTools-package
TFFM	TFFM-class
TFFMDetail	TFFM-class
TFFMFirst	TFFM-class
toGRangesList	toGRangesList-methods
toGRangesList,SitePairSetList,Axt-method	toGRangesList-methods
toGRangesList-methods	toGRangesList-methods
toICM	toICM-methods
toICM,character-method	toICM-methods
toICM,DNAStringSet-method	toICM-methods
toICM,matrix-method	toICM-methods
toICM,PFMatrix-method	toICM-methods
toICM,PFMatrixList-method	toICM-methods
toPWM	toPWM-methods
toPWM,character-method	toPWM-methods
toPWM,DNAStringSet-method	toPWM-methods
toPWM,matrix-method	toPWM-methods
toPWM,PFMatrix-method	toPWM-methods
toPWM,PFMatrixList-method	toPWM-methods
totalIC	XMatrix-class
totalIC,ICMatrix-method	XMatrix-class
totalIC,TFFM-method	TFFM-class
totalIC-methods	XMatrix-class
views	SiteSet-class
views,SiteSet-method	SiteSet-class
writeGFF2	writeGFF3-methods
writeGFF2,SitePairSet-method	writeGFF3-methods
writeGFF2,SitePairSetList-method	writeGFF3-methods
writeGFF2,SiteSet-method	writeGFF3-methods
writeGFF2,SiteSetList-method	writeGFF3-methods
writeGFF2-methods	writeGFF3-methods
writeGFF3	writeGFF3-methods
writeGFF3,SitePairSet-method	writeGFF3-methods
writeGFF3,SitePairSetList-method	writeGFF3-methods
writeGFF3,SiteSet-method	writeGFF3-methods
writeGFF3,SiteSetList-method	writeGFF3-methods
writeGFF3-methods	writeGFF3-methods
XMatrix	XMatrix-class
XMatrix-class	XMatrix-class
XMatrixList	XMatrixList-class
XMatrixList,list-method	XMatrixList-class
[,MotifSet,ANY,ANY,ANY-method	MotifSet-class
[,MotifSet,ANY,ANY-method	MotifSet-class
[,MotifSet-method	MotifSet-class
[,SiteSet,ANY,ANY,ANY-method	SiteSet-class
[,SiteSet,ANY,ANY-method	SiteSet-class
[,SiteSet-method	SiteSet-class
[-methods	XMatrix-class
