calculateBatchRPM	calculateBatchRPM
calculateBatchRPM,r3CseqInBatch-method	calculateBatchRPM
calculateRPM	calculateRPM
calculateRPM,r3Cseq-method	calculateRPM
contrCoverage	contrCoverage
contrCoverage,r3Cseq-method	contrCoverage
contrInteractionRegions	contrInteractionRegions
contrInteractionRegions,r3CseqCommon-method	contrInteractionRegions
contrRawData	contrRawData
contrRawData,r3Cseq-method	contrRawData
contrRawData<-	contrRawData
contrRawData<-,r3Cseq-method	contrRawData
contrReadCount	contrReadCount
contrReadCount,r3CseqCommon-method	contrReadCount
contrRPM	contrRPM
contrRPM,r3CseqCommon-method	contrRPM
enzymeDb	enzymeDb
expCoverage	expCoverage
expCoverage,r3Cseq-method	expCoverage
expInteractionRegions	expInteractionRegions
expInteractionRegions,r3CseqCommon-method	expInteractionRegions
export3Cseq2bedGraph	export3Cseq2bedGraph
export3Cseq2bedGraph,r3Cseq-method	export3Cseq2bedGraph
export3CseqRawReads2bedGraph	export3CseqRawReads2bedGraph
export3CseqRawReads2bedGraph,r3Cseq-method	export3CseqRawReads2bedGraph
exportBatchInteractions2text	exportBatchInteractions2text
exportBatchInteractions2text,r3CseqInBatch-method	exportBatchInteractions2text
exportInteractions2text	exportInteractions2text
exportInteractions2text,r3Cseq-method	exportInteractions2text
expRawData	expRawData
expRawData,r3Cseq-method	expRawData
expRawData<-	expRawData
expRawData<-,r3Cseq-method	expRawData
expReadCount	expReadCount
expReadCount,r3CseqCommon-method	expReadCount
expRPM	expRPM
expRPM,r3CseqCommon-method	expRPM
generate3CseqReport	generate3CseqReport
generate3CseqReport,r3Cseq-method	generate3CseqReport
generate3CseqReport,r3CseqInBatch-method	generate3CseqReport
getBatchInteractions	getBatchInteractions
getBatchInteractions,r3CseqInBatch-method	getBatchInteractions
getBatchRawReads	getBatchRawReads
getBatchRawReads,r3CseqInBatch-method	getBatchRawReads
getBatchReadCountPerRestrictionFragment	getBatchReadCountPerRestrictionFragment
getBatchReadCountPerRestrictionFragment,r3CseqInBatch-method	getBatchReadCountPerRestrictionFragment
getBatchReadCountPerWindow	getBatchReadCountPerWindow
getBatchReadCountPerWindow,r3CseqInBatch-method	getBatchReadCountPerWindow
getContrInteractionsInRefseq	getContrInteractionsInRefseq
getContrInteractionsInRefseq,r3Cseq-method	getContrInteractionsInRefseq
getCoverage	getCoverage
getCoverage,r3Cseq-method	getCoverage
getExpInteractionsInRefseq	getExpInteractionsInRefseq
getExpInteractionsInRefseq,r3Cseq-method	getExpInteractionsInRefseq
getInteractions	getInteractions
getInteractions,r3Cseq-method	getInteractions
getRawReads	getRawReads
getRawReads,r3Cseq-method	getRawReads
getReadCountPerRestrictionFragment	getReadCountPerRestrictionFragment
getReadCountPerRestrictionFragment,r3Cseq-method	getReadCountPerRestrictionFragment
getReadCountPerWindow	getReadCountPerWindow
getReadCountPerWindow,r3Cseq-method	getReadCountPerWindow
getViewpoint	getViewpoint
getViewpoint,r3Cseq-method	getViewpoint
hg18refGene	hg18refGene
hg19refGene	hg19refGene
mm10refGene	mm10refGene
mm9refGene	mm9refGene
Myb_prom_FB	Myb_prom_FB
Myb_prom_FL	Myb_prom_FL
plot3Cecdf	plot3Cecdf
plot3Cecdf,r3Cseq-method	plot3Cecdf
plotDomainogramNearViewpoint	plotDomainogramNearViewpoint
plotDomainogramNearViewpoint,r3Cseq-method	plotDomainogramNearViewpoint
plotInteractionsNearViewpoint	plotInteractionsNearViewpoint
plotInteractionsNearViewpoint,r3Cseq-method	plotInteractionsNearViewpoint
plotInteractionsPerChromosome	plotInteractionsPerChromosome
plotInteractionsPerChromosome,r3Cseq-method	plotInteractionsPerChromosome
plotOverviewInteractions	plotOverviewInteractions
plotOverviewInteractions,r3Cseq-method	plotOverviewInteractions
r3Cseq	r3Cseq-class
r3Cseq-class	r3Cseq-class
r3CseqCommon	r3CseqCommon-class
r3CseqCommon-class	r3CseqCommon-class
r3CseqInBatch	r3CseqInBatch-class
r3CseqInBatch-class	r3CseqInBatch-class
rn5refGene	rn5refGene
