All functions
addGCBias	addGCBias
annotationMatches annotationMatches<-	annotationMatches
assembleKmers	assembleKmers
cbind	cbind method for chromVARDeviations
chromVAR_theme	chromVAR_theme
chromVAR	chromVAR: A package for computing variability across sets of peaks.
chromVARDeviations-class	chromVARDeviations
computeDeviations	computeDeviations
computeExpectations	computeExpectations
computeVariability	computeVariability
counts counts<-	Accessors for the 'counts' slot of a SummarizedExperiment
deviations	deviations
deviationScores	deviationScores
deviationsCovariability	deviationsCovariability
deviationsTsne	deviationsTsne
differentialDeviations	differentialDeviations
differentialVariability	differentialVariability
data	example_counts
filterPeaks	filterPeaks
filterSamples	filterSamples
filterSamplesPlot	filterSamplesPlot
getAnnotationCorrelation	getAnnotationCorrelation
getAnnotations	getAnnotations
getAnnotationSynergy	getAnnotationSynergy
getBackgroundPeaks	getBackgroundPeaks
getCisGroups	getCisGroups
getCounts	getCounts
getFragmentsPerPeak	getFragmentsPerPeak
getFragmentsPerSample	getFragmentsPerSample
getJasparMotifs	getJasparMotifs
getPeaks	getPeaks
getPermutedData	getPermutedData
getSampleCorrelation	getSampleCorrelation
getSampleDepths	getSampleDepths
getSampleDistance	getSampleDistance
getTotalFragments	getTotalFragments
makeBiasBins	makeBiasBins
makePermutedSets	makePermutedSets
matchKmers	matchKmers
data	mini_counts
data	mini_dev
data	mini_ix
plotDeviationsTsne	plotDeviationsTsne
plotKmerMismatch	plotKmerMismatch
plotVariability	plotVariability
pwmDistance	pwmDistance
rbind	rbind method chromVARDeviations
readNarrowpeaks	readNarrowpeaks