chromVAR-package	chromVAR
addGCBias	addGCBias
addGCBias,RangedSummarizedExperiment-method	addGCBias
addGCBias,SummarizedExperiment-method	addGCBias
annoation_matches<-,SummarizedExperiment-method	annotationMatches
annotationMatches	annotationMatches
annotationMatches,SummarizedExperiment-method	annotationMatches
annotationMatches<-	annotationMatches
annotationMatches<-,SummarizedExperiment-method	annotationMatches
assembleKmers	assembleKmers
cbind,chromVARDeviations-method	cbind-chromVARDeviations-method
chromVAR	chromVAR
chromVARDeviations-class	chromVARDeviations-class
chromVAR_theme	chromVAR_theme
computeDeviations	computeDeviations
computeDeviations,MatrixOrmatrix,list-method	computeDeviations
computeDeviations,MatrixOrmatrix,MatrixOrmatrix-method	computeDeviations
computeDeviations,MatrixOrmatrix,missingOrNULL-method	computeDeviations
computeDeviations,MatrixOrmatrix,SummarizedExperiment-method	computeDeviations
computeDeviations,SummarizedExperiment,list-method	computeDeviations
computeDeviations,SummarizedExperiment,MatrixOrmatrix-method	computeDeviations
computeDeviations,SummarizedExperiment,missingOrNULL-method	computeDeviations
computeDeviations,SummarizedExperiment,SummarizedExperiment-method	computeDeviations
computeExpectations	computeExpectations
computeExpectations,MatrixOrmatrix-method	computeExpectations
computeExpectations,SummarizedExperiment-method	computeExpectations
computeVariability	computeVariability
counts,SummarizedExperiment-method	counts
counts<-,SummarizedExperiment,MatrixOrmatrix-method	counts
counts<-,SummarizedExperiment-method	counts
deviations	deviations
deviations,chromVARDeviations-method	deviations
deviationScores	deviationScores
deviationScores,chromVARDeviations-method	deviationScores
deviationsCovariability	deviationsCovariability
deviationsTsne	deviationsTsne
differentialDeviations	differentialDeviations
differentialVariability	differentialVariability
example_counts	example_counts
filterPeaks	filterPeaks
filterSamples	filterSamples
filterSamplesPlot	filterSamplesPlot
getAnnotationCorrelation	getAnnotationCorrelation
getAnnotationCorrelation,MatrixOrmatrix,list-method	getAnnotationCorrelation
getAnnotationCorrelation,MatrixOrmatrix,MatrixOrmatrix-method	getAnnotationCorrelation
getAnnotationCorrelation,MatrixOrmatrix,SummarizedExperiment-method	getAnnotationCorrelation
getAnnotationCorrelation,SummarizedExperiment,list-method	getAnnotationCorrelation
getAnnotationCorrelation,SummarizedExperiment,MatrixOrmatrix-method	getAnnotationCorrelation
getAnnotationCorrelation,SummarizedExperiment,SummarizedExperiment-method	getAnnotationCorrelation
getAnnotations	getAnnotations
getAnnotations,character-method	getAnnotations
getAnnotations,data.frame-method	getAnnotations
getAnnotations,GRangesList-method	getAnnotations
getAnnotations,list-method	getAnnotations
getAnnotations,MatrixOrmatrix-method	getAnnotations
getAnnotationSynergy	getAnnotationSynergy
getAnnotationSynergy,MatrixOrmatrix,list-method	getAnnotationSynergy
getAnnotationSynergy,MatrixOrmatrix,MatrixOrmatrix-method	getAnnotationSynergy
getAnnotationSynergy,MatrixOrmatrix,SummarizedExperiment-method	getAnnotationSynergy
getAnnotationSynergy,SummarizedExperiment,list-method	getAnnotationSynergy
getAnnotationSynergy,SummarizedExperiment,MatrixOrmatrix-method	getAnnotationSynergy
getAnnotationSynergy,SummarizedExperiment,SummarizedExperiment-method	getAnnotationSynergy
getBackgroundPeaks	getBackgroundPeaks
getBackgroundPeaks,MatrixOrmatrix-method	getBackgroundPeaks
getBackgroundPeaks,RangedSummarizedExperiment-method	getBackgroundPeaks
getBackgroundPeaks,SummarizedExperiment-method	getBackgroundPeaks
getCisGroups	getCisGroups
getCisGroups,GenomicRanges-method	getCisGroups
getCisGroups,RangedSummarizedExperiment-method	getCisGroups
getCounts	getCounts
getFragmentsPerPeak	getFragmentsPerPeak
getFragmentsPerPeak,MatrixOrmatrix-method	getFragmentsPerPeak
getFragmentsPerPeak,SummarizedExperiment-method	getFragmentsPerPeak
getFragmentsPerSample	getFragmentsPerSample
getFragmentsPerSample,MatrixOrmatrix-method	getFragmentsPerSample
getFragmentsPerSample,SummarizedExperiment-method	getFragmentsPerSample
getJasparMotifs	getJasparMotifs
getPeaks	getPeaks
getPermutedData	getPermutedData
getSampleCorrelation	getSampleCorrelation
getSampleDepths	getSampleDepths
getSampleDistance	getSampleDistance
getTotalFragments	getTotalFragments
getTotalFragments,MatrixOrmatrix-method	getTotalFragments
getTotalFragments,SummarizedExperiment-method	getTotalFragments
makeBiasBins	makeBiasBins
makeBiasBins,MatrixOrmatrix-method	makeBiasBins
makeBiasBins,RangedSummarizedExperiment-method	makeBiasBins
makeBiasBins,SummarizedExperiment-method	makeBiasBins
makePermutedSets	makePermutedSets
makePermutedSets,MatrixOrmatrix,list-method	makePermutedSets
makePermutedSets,MatrixOrmatrix,MatrixOrmatrix-method	makePermutedSets
makePermutedSets,MatrixOrmatrix,SummarizedExperiment-method	makePermutedSets
makePermutedSets,RangedSummarizedExperiment,list-method	makePermutedSets
makePermutedSets,RangedSummarizedExperiment,MatrixOrmatrix-method	makePermutedSets
makePermutedSets,RangedSummarizedExperiment,SummarizedExperiment-method	makePermutedSets
makePermutedSets,SummarizedExperiment,list-method	makePermutedSets
makePermutedSets,SummarizedExperiment,MatrixOrmatrix-method	makePermutedSets
makePermutedSets,SummarizedExperiment,SummarizedExperiment-method	makePermutedSets
matchKmers	matchKmers
matchKmers,character,character-method	matchKmers
matchKmers,character,DNAString-method	matchKmers
matchKmers,character,DNAStringSet-method	matchKmers
matchKmers,character,GenomicRanges-method	matchKmers
matchKmers,character,RangedSummarizedExperiment-method	matchKmers
matchKmers,DNAString,ANY-method	matchKmers
matchKmers,DNAStringSet,ANY-method	matchKmers
matchKmers,numeric,ANY-method	matchKmers
mini_counts	mini_counts
mini_dev	mini_dev
mini_ix	mini_ix
plotDeviationsTsne	plotDeviationsTsne
plotKmerMismatch	plotKmerMismatch
plotVariability	plotVariability
pwmDistance	pwmDistance
rbind,chromVARDeviations-method	rbind-chromVARDeviations-method
readNarrowpeaks	readNarrowpeaks
