addLogo	addLogo
addMotifAnnotation	addMotifAnnotation
addSignificantGenes	addSignificantGenes
addSignificantGenes,character-method	addSignificantGenes
addSignificantGenes,GeneSet-method	addSignificantGenes
addSignificantGenes,GeneSetCollection-method	addSignificantGenes
addSignificantGenes,list-method	addSignificantGenes
aucScores	aucScores-class
aucScores-class	aucScores-class
calcAUC	calcAUC
calcAUC,character-method	calcAUC
calcAUC,GeneSet-method	calcAUC
calcAUC,GeneSetCollection-method	calcAUC
calcAUC,list-method	calcAUC
cisTarget	RcisTarget
colnames,rankingRcisTarget-method	rankingRcisTarget-class
convertToTargetRegions	convertToTargetRegions
dbRegionsLoc	dbRegionsLoc
dbRegionsLoc_hg19	dbRegionsLoc
dbRegionsLoc_mm9	dbRegionsLoc
getAUC	aucScores-class
getAUC,aucScores-method	aucScores-class
getColumnNames	importRankings
getDbRegionsLoc	getDbRegionsLoc
getMaxRank	rankingRcisTarget-class
getMaxRank,rankingRcisTarget-method	rankingRcisTarget-class
getMotifAnnotation	getMotifAnnotation
getNumColsInDB	rankingRcisTarget-class
getNumColsInDB,rankingRcisTarget-method	rankingRcisTarget-class
getRanking	rankingRcisTarget-class
getRanking,rankingRcisTarget-method	rankingRcisTarget-class
getRowNames	importRankings
getSignificantGenes	addSignificantGenes
getSignificantGenes,character-method	addSignificantGenes
getSignificantGenes,factor-method	addSignificantGenes
getSignificantGenes,GeneSet-method	addSignificantGenes
getSignificantGenes,GeneSetCollection-method	addSignificantGenes
getSignificantGenes,list-method	addSignificantGenes
importAnnotations	importAnnotations
importRankings	importRankings
motifAnnotations	motifAnnotations
motifAnnotations_dmel	motifAnnotations
motifAnnotations_dmel_v8	motifAnnotations
motifAnnotations_hgnc	motifAnnotations
motifAnnotations_hgnc_v8	motifAnnotations
motifAnnotations_mgi	motifAnnotations
motifAnnotations_mgi_v8	motifAnnotations
ncol,rankingRcisTarget-method	rankingRcisTarget-class
nrow,rankingRcisTarget-method	rankingRcisTarget-class
rankingRcisTarget	rankingRcisTarget-class
rankingRcisTarget-class	rankingRcisTarget-class
reRank	reRank
rownames,rankingRcisTarget-method	rankingRcisTarget-class
show,aucScores-method	aucScores-class
show,rankingRcisTarget-method	rankingRcisTarget-class
