averageBindingValues	averageBindingValues
averageBindingValues<-	averageBindingValues
averageBindingValues<-,ChIPSeqSpikeCore-method	averageBindingValues
averageBindingValues<-,ChIPSeqSpikeDataset-method	averageBindingValues
averageBindingValues<-,ChIPSeqSpikeDatasetBoost-method	averageBindingValues
bigWigFile	bigWigFile
bigWigFile<-	bigWigFile
bigWigFile<-,ChIPSeqSpikeCore-method	bigWigFile
bigWigFile<-,ChIPSeqSpikeDataset-method	bigWigFile
bigWigFile<-,ChIPSeqSpikeDatasetBoost-method	bigWigFile
bigWigFile<-,Experiment-method	bigWigFile
bigWigFile<-,ExperimentLoaded-method	bigWigFile
boxplotSpike	boxplotSpike
boxplotSpike,ChIPSeqSpikeDataset-method	boxplotSpike
boxplotSpike,ChIPSeqSpikeDatasetBoost-method	boxplotSpike
boxplotSpike,ChIPSeqSpikeDatasetList-method	boxplotSpike
boxplotSpike,ChIPSeqSpikeDatasetListBoost-method	boxplotSpike
ChIPSeqSpikeCore	ChIPSeqSpikeCore
ChIPSeqSpikeCore-class	ChIPSeqSpikeCore
ChIPSeqSpikeDataset	ChIPSeqSpikeDataset-class
ChIPSeqSpikeDataset-class	ChIPSeqSpikeDataset-class
ChIPSeqSpikeDatasetBoost	ChIPSeqSpikeDatasetBoost-class
ChIPSeqSpikeDatasetBoost-class	ChIPSeqSpikeDatasetBoost-class
ChIPSeqSpikeDatasetList	ChIPSeqSpikeDatasetList-class
ChIPSeqSpikeDatasetList-class	ChIPSeqSpikeDatasetList-class
ChIPSeqSpikeDatasetListBoost	ChIPSeqSpikeDatasetListBoost-class
ChIPSeqSpikeDatasetListBoost-class	ChIPSeqSpikeDatasetListBoost-class
count	count
count<-	count
count<-,ChIPSeqSpikeCore-method	count
count<-,ChIPSeqSpikeDataset-method	count
count<-,ChIPSeqSpikeDatasetBoost-method	count
count<-,Experiment-method	count
count<-,ExperimentLoaded-method	count
csds	result_data
datasetList	datasetList
datasetList<-	datasetList
datasetList<-,ChIPSeqSpikeDatasetList-method	datasetList
datasetList<-,ChIPSeqSpikeDatasetListBoost-method	datasetList
estimateScalingFactors	estimateScalingFactors
estimateScalingFactors,ChIPSeqSpikeDataset-method	estimateScalingFactors
estimateScalingFactors,ChIPSeqSpikeDatasetBoost-method	estimateScalingFactors
estimateScalingFactors,ChIPSeqSpikeDatasetList-method	estimateScalingFactors
estimateScalingFactors,ChIPSeqSpikeDatasetListBoost-method	estimateScalingFactors
estimateScalingFactors,Experiment-method	estimateScalingFactors
estimateScalingFactors,ExperimentLoaded-method	estimateScalingFactors
exoCount	exoCount
exoCount<-	exoCount
exoCount<-,Experiment-method	exoCount
exoCount<-,ExperimentLoaded-method	exoCount
exogenousScalingFactor	exogenousScalingFactor
exogenousScalingFactor<-	exogenousScalingFactor
exogenousScalingFactor<-,Experiment-method	exogenousScalingFactor
exogenousScalingFactor<-,ExperimentLoaded-method	exogenousScalingFactor
Experiment	Experiment-class
Experiment-class	Experiment-class
experimentList	experimentList
experimentList<-	experimentList
experimentList<-,ChIPSeqSpikeDataset-method	experimentList
experimentList<-,ChIPSeqSpikeDatasetBoost-method	experimentList
ExperimentLoaded	ExperimentLoaded-class
ExperimentLoaded-class	ExperimentLoaded-class
exportBigWigs	exportBigWigs
exportBigWigs,ChIPSeqSpikeDatasetBoost-method	exportBigWigs
exportBigWigs,ChIPSeqSpikeDatasetListBoost-method	exportBigWigs
extractBinding	extractBinding
extractBinding,ChIPSeqSpikeDataset-method	extractBinding
extractBinding,ChIPSeqSpikeDatasetBoost-method	extractBinding
extractBinding,ChIPSeqSpikeDatasetList-method	extractBinding
extractBinding,ChIPSeqSpikeDatasetListBoost-method	extractBinding
getAverageBindingValues	getAverageBindingValues
getAverageBindingValues,ChIPSeqSpikeCore-method	getAverageBindingValues
getAverageBindingValues,ChIPSeqSpikeDataset-method	getAverageBindingValues
getAverageBindingValues,ChIPSeqSpikeDatasetBoost-method	getAverageBindingValues
getBam	getBam
getBam,ChIPSeqSpikeCore-method	getBam
getBam,ChIPSeqSpikeDataset-method	getBam
getBam,ChIPSeqSpikeDatasetBoost-method	getBam
getBam,Experiment-method	getBam
getBam,ExperimentLoaded-method	getBam
getBigWigFile	getBigWigFile
getBigWigFile,ChIPSeqSpikeCore-method	getBigWigFile
getBigWigFile,ChIPSeqSpikeDataset-method	getBigWigFile
getBigWigFile,ChIPSeqSpikeDatasetBoost-method	getBigWigFile
getBigWigFile,ChIPSeqSpikeDatasetList-method	getBigWigFile
getBigWigFile,Experiment-method	getBigWigFile
getBigWigFile,ExperimentLoaded-method	getBigWigFile
getCount	getCount
getCount,ChIPSeqSpikeCore-method	getCount
getCount,ChIPSeqSpikeDataset-method	getCount
getCount,ChIPSeqSpikeDatasetBoost-method	getCount
getCount,Experiment-method	getCount
getCount,ExperimentLoaded-method	getCount
getDatasetList	getDatasetList
getDatasetList,ChIPSeqSpikeDatasetList-method	getDatasetList
getDatasetList,ChIPSeqSpikeDatasetListBoost-method	getDatasetList
getExoCount	getExoCount
getExoCount,Experiment-method	getExoCount
getExoCount,ExperimentLoaded-method	getExoCount
getExogenousBam	getExogenousBam
getExogenousBam,Experiment-method	getExogenousBam
getExogenousBam,ExperimentLoaded-method	getExogenousBam
getExogenousScalingFactor	getExogenousScalingFactor
getExogenousScalingFactor,Experiment-method	getExogenousScalingFactor
getExogenousScalingFactor,ExperimentLoaded-method	getExogenousScalingFactor
getExperimentList	getExperimentList
getExperimentList,ChIPSeqSpikeDataset-method	getExperimentList
getExperimentList,ChIPSeqSpikeDatasetBoost-method	getExperimentList
getExperimentListBigWigs	getExperimentListBigWigs
getExperimentListBigWigs,ChIPSeqSpikeDataset-method	getExperimentListBigWigs
getExperimentListBigWigs,ChIPSeqSpikeDatasetBoost-method	getExperimentListBigWigs
getExpName	getExpName
getExpName,ChIPSeqSpikeDataset-method	getExpName
getExpName,ChIPSeqSpikeDatasetBoost-method	getExpName
getExpName,Experiment-method	getExpName
getExpName,ExperimentLoaded-method	getExpName
getLoadedData	getLoadedData
getLoadedData,ChIPSeqSpikeDatasetBoost-method	getLoadedData
getLoadedData,ExperimentLoaded-method	getLoadedData
getMatBindingValues	getMatBindingValues
getMatBindingValues,ChIPSeqSpikeCore-method	getMatBindingValues
getMatBindingValues,ChIPSeqSpikeDataset-method	getMatBindingValues
getMatBindingValues,ChIPSeqSpikeDatasetBoost-method	getMatBindingValues
getRatio	getRatio
getRatio,ChIPSeqSpikeDataset-method	getRatio
getRatio,ChIPSeqSpikeDatasetBoost-method	getRatio
getRatio,ChIPSeqSpikeDatasetList-method	getRatio
getRatio,ChIPSeqSpikeDatasetListBoost-method	getRatio
getRatio,Experiment-method	getRatio
getRatio,ExperimentLoaded-method	getRatio
getScalingFactor	getScalingFactor
getScalingFactor,ChIPSeqSpikeCore-method	getScalingFactor
getScalingFactor,ChIPSeqSpikeDataset-method	getScalingFactor
getScalingFactor,ChIPSeqSpikeDatasetBoost-method	getScalingFactor
getScalingFactor,Experiment-method	getScalingFactor
getScalingFactor,ExperimentLoaded-method	getScalingFactor
inputSubtraction	inputSubtraction
inputSubtraction,ChIPSeqSpikeDataset-method	inputSubtraction
inputSubtraction,ChIPSeqSpikeDatasetBoost-method	inputSubtraction
inputSubtraction,ChIPSeqSpikeDatasetList-method	inputSubtraction
inputSubtraction,ChIPSeqSpikeDatasetListBoost-method	inputSubtraction
matBindingValues	matBindingValues
matBindingValues<-	matBindingValues
matBindingValues<-,ChIPSeqSpikeCore-method	matBindingValues
matBindingValues<-,ChIPSeqSpikeDataset-method	matBindingValues
matBindingValues<-,ChIPSeqSpikeDatasetBoost-method	matBindingValues
plotCor	plotCor
plotCor,ChIPSeqSpikeDataset-method	plotCor
plotCor,ChIPSeqSpikeDatasetBoost-method	plotCor
plotCor,ChIPSeqSpikeDatasetList-method	plotCor
plotCor,ChIPSeqSpikeDatasetListBoost-method	plotCor
plotHeatmaps	plotHeatmaps
plotHeatmaps,ChIPSeqSpikeDataset-method	plotHeatmaps
plotHeatmaps,ChIPSeqSpikeDatasetBoost-method	plotHeatmaps
plotHeatmaps,ChIPSeqSpikeDatasetList-method	plotHeatmaps
plotHeatmaps,ChIPSeqSpikeDatasetListBoost-method	plotHeatmaps
plotProfile	plotProfile
plotProfile,ChIPSeqSpikeDataset-method	plotProfile
plotProfile,ChIPSeqSpikeDatasetBoost-method	plotProfile
plotProfile,ChIPSeqSpikeDatasetList-method	plotProfile
plotProfile,ChIPSeqSpikeDatasetListBoost-method	plotProfile
plotTransform	plotTransform
plotTransform,ChIPSeqSpikeDataset-method	plotTransform
plotTransform,ChIPSeqSpikeDatasetList-method	plotTransform
ratio	ratio
result_data	result_data
result_estimateScalingFactors	result_data
result_extractBinding	result_data
scaling	scaling
scaling,ChIPSeqSpikeDataset-method	scaling
scaling,ChIPSeqSpikeDatasetBoost-method	scaling
scaling,ChIPSeqSpikeDatasetList-method	scaling
scaling,ChIPSeqSpikeDatasetListBoost-method	scaling
scalingFactor	scalingFactor
scalingFactor<-	scalingFactor
scalingFactor<-,ChIPSeqSpikeCore-method	scalingFactor
scalingFactor<-,ChIPSeqSpikeDataset-method	scalingFactor
scalingFactor<-,ChIPSeqSpikeDatasetBoost-method	scalingFactor
scalingFactor<-,Experiment-method	scalingFactor
scalingFactor<-,ExperimentLoaded-method	scalingFactor
spikeDataset	spikeDataset
spikePipe	spikePipe
spikeSummary	spikeSummary
spikeSummary,ChIPSeqSpikeDataset-method	spikeSummary
spikeSummary,ChIPSeqSpikeDatasetBoost-method	spikeSummary
spikeSummary,ChIPSeqSpikeDatasetList-method	spikeSummary
spikeSummary,ChIPSeqSpikeDatasetListBoost-method	spikeSummary
spikeSummary,Experiment-method	spikeSummary
spikeSummary,ExperimentLoaded-method	spikeSummary
[[,ChIPSeqSpikeDataset,ANY,ANY-method	ChIPSeqSpikeDataset-class
[[,ChIPSeqSpikeDatasetList,ANY,ANY-method	ChIPSeqSpikeDatasetList-class
[[,ChIPSeqSpikeDatasetListBoost,ANY,ANY-method	ChIPSeqSpikeDatasetListBoost-class
[[<-,ChIPSeqSpikeDataset,ANY,ANY-method	ChIPSeqSpikeDataset-class
[[<-,ChIPSeqSpikeDatasetList,ANY,ANY-method	ChIPSeqSpikeDatasetList-class
[[<-,Experiment,ANY,ANY-method	Experiment-class
