annotateWithFeature	annotateWithFeature-methods
annotateWithFeature,GRanges,GRanges-method	annotateWithFeature-methods
annotateWithFeatureFlank	annotateWithFeatureFlank-methods
annotateWithFeatureFlank,GRanges,GRanges,GRanges-method	annotateWithFeatureFlank-methods
annotateWithFeatures	annotateWithFeatures-methods
annotateWithFeatures,GRanges,GRangesList-method	annotateWithFeatures-methods
annotateWithFeatures,GRangesList,GRangesList-method	annotateWithFeatures-methods
annotateWithGeneParts	annotateWithGeneParts-methods
annotateWithGeneParts,GRanges,GRangesList-method	annotateWithGeneParts-methods
annotateWithGeneParts,GRangesList,GRangesList-method	annotateWithGeneParts-methods
AnnotationByFeature-class	AnnotationByFeature-class
AnnotationByGeneParts-class	AnnotationByGeneParts-class
AnnotationByGeneParts-method	AnnotationByGeneParts-methods
binMatrix	binMatrix-methods
binMatrix,ScoreMatrix-method	binMatrix-methods
binMatrix,ScoreMatrixList-method	binMatrix-methods
cage	cage
calculateOverlapSignificance	calculateOverlapSignificance-methods
calculateOverlapSignificance,GRanges,GRanges-method	calculateOverlapSignificance-methods
convertBed2Exons	convertBed2Exons-methods
convertBed2Exons,data.frame-method	convertBed2Exons-methods
convertBed2Introns	convertBed2Introns-methods
convertBed2Introns,data.frame-method	convertBed2Introns-methods
convertBedDf	convertBedDf-methods
convertBedDf,data.frame-method	convertBedDf-methods
cpgi	cpgi
extract,ScoreMatrix,ANY-method	sub-ScoreMatrix-ANY-ANY-method
findFeatureComb	findFeatureComb-methods
findFeatureComb,GRangesList-method	findFeatureComb-methods
genes	genes
getAssociationWithTSS	AnnotationByGeneParts-methods
getAssociationWithTSS,	AnnotationByGeneParts-methods
getAssociationWithTSS,-methods	AnnotationByGeneParts-methods
getAssociationWithTSS,AnnotationByGeneParts-method	AnnotationByGeneParts-methods
getFeatsWithTargetsStats	getFeatsWithTargetsStats-methods
getFeatsWithTargetsStats,AnnotationByFeature-method	getFeatsWithTargetsStats-methods
getFlanks	getFlanks-methods
getFlanks,GRanges-method	getFlanks-methods
getMembers	getMembers-methods
getMembers,AnnotationByFeature-method	getMembers-methods
getRandomEnrichment	getRandomEnrichment-methods
getRandomEnrichment,GRanges,GRanges-method	getRandomEnrichment-methods
getTargetAnnotationStats	getTargetAnnotationStats-methods
getTargetAnnotationStats,AnnotationByFeature-method	getTargetAnnotationStats-methods
gffToGRanges	gffToGRanges
heatMatrix	heatMatrix
heatMeta	heatMeta
heatTargetAnnotation	heatTargetAnnotation-methods
intersectScoreMatrixList	intersectScoreMatrixList-methods
intersectScoreMatrixList,ScoreMatrixList-method	intersectScoreMatrixList-methods
multiHeatMatrix	multiHeatMatrix
Ops,numeric,ScoreMatrixList-method	Ops-numeric-ScoreMatrixList-method
Ops,ScoreMatrix,ScoreMatrix-method	Ops-ScoreMatrix-ScoreMatrix-method
Ops,ScoreMatrixList,numeric-method	Ops-ScoreMatrixList-numeric-method
Ops,ScoreMatrixList,ScoreMatrixList-method	Ops-ScoreMatrixList-ScoreMatrixList-method
orderBy	orderBy-methods
orderBy,ScoreMatrixList-method	orderBy-methods
patternMatrix	patternMatrix-methods
patternMatrix,character,DNAStringSet,ANY-method	patternMatrix-methods
patternMatrix,character,DNAStringSet-method	patternMatrix-methods
patternMatrix,character,GRanges,BSgenome-method	patternMatrix-methods
patternMatrix,list,DNAStringSet,ANY-method	patternMatrix-methods
patternMatrix,list,DNAStringSet-method	patternMatrix-methods
patternMatrix,list,GRanges,BSgenome-method	patternMatrix-methods
patternMatrix,matrix,DNAStringSet,ANY-method	patternMatrix-methods
patternMatrix,matrix,DNAStringSet-method	patternMatrix-methods
patternMatrix,matrix,GRanges,BSgenome-method	patternMatrix-methods
plotGeneAnnotation	heatTargetAnnotation-methods
plotMeta	plotMeta
plotTargetAnnotation	plotTargetAnnotation-methods
plotTargetAnnotation,AnnotationByFeature-method	plotTargetAnnotation-methods
promoters	promoters
RandomEnrichment-class	RandomEnrichment-class
randomizeFeature	randomizeFeature-methods
randomizeFeature,GRanges-method	randomizeFeature-methods
readBed	readBed
readBroadPeak	readBroadPeak
readFeatureFlank	readFeatureFlank-methods
readFeatureFlank,character-method	readFeatureFlank-methods
readGeneric	readGeneric
readNarrowPeak	readNarrowPeak
readTranscriptFeatures	readTranscriptFeatures-methods
readTranscriptFeatures,character-method	readTranscriptFeatures-methods
scaleScoreMatrix	scaleScoreMatrix-methods
scaleScoreMatrix,ScoreMatrix-method	scaleScoreMatrix-methods
scaleScoreMatrixList	scaleScoreMatrixList
scaleScoreMatrixList,ScoreMatrixList-method	scaleScoreMatrixList
ScoreMatrix	ScoreMatrix-methods
ScoreMatrix,character,GRanges-method	ScoreMatrix-methods
ScoreMatrix,GRanges,GRanges-method	ScoreMatrix-methods
ScoreMatrix,RleList,GRanges-method	ScoreMatrix-methods
ScoreMatrix-class	ScoreMatrix-class
ScoreMatrixBin	ScoreMatrixBin-methods
ScoreMatrixBin,character,GRanges-method	ScoreMatrixBin-methods
ScoreMatrixBin,character,GRangesList-method	ScoreMatrixBin-methods
ScoreMatrixBin,GRanges,GRanges-method	ScoreMatrixBin-methods
ScoreMatrixBin,GRanges,GRangesList-method	ScoreMatrixBin-methods
ScoreMatrixBin,RleList,GRanges-method	ScoreMatrixBin-methods
ScoreMatrixBin,RleList,GRangesList-method	ScoreMatrixBin-methods
ScoreMatrixList	ScoreMatrixList-methods
ScoreMatrixList-class	ScoreMatrixList-class
show,AnnotationByFeature-method	show-methods
show,AnnotationByGeneParts-method	show-methods
show,RandomEnrichment-method	show-methods
show,ScoreMatrix-method	show-methods
show,ScoreMatrixList-method	show-methods
[,ScoreMatrix,ANY,ANY,ANY-method	sub-ScoreMatrix-ANY-ANY-ANY-method
[,ScoreMatrix,ANY,ANY-method	sub-ScoreMatrix-ANY-ANY-method
[,ScoreMatrix-method	sub-ScoreMatrix-ANY-ANY-ANY-method
[,ScoreMatrixList,ANY,ANY,ANY-method	sub-ScoreMatrixList-ANY-ANY-ANY-method
[,ScoreMatrixList-method	sub-ScoreMatrixList-ANY-ANY-ANY-method
