addGCBias               addGCBias
annotationMatches       annotationMatches
assembleKmers           assembleKmers
cbind,chromVARDeviations-method
                        cbind method for chromVARDeviations
chromVAR                chromVAR: A package for computing variability
                        across sets of peaks.
chromVARDeviations-class
                        chromVARDeviations
chromVAR_theme          chromVAR_theme
computeDeviations       computeDeviations
computeExpectations     computeExpectations
computeVariability      computeVariability
counts,SummarizedExperiment-method
                        Accessors for the 'counts' slot of a
                        SummarizedExperiment
deviationScores         deviationScores
deviations              deviations
deviationsCovariability
                        deviationsCovariability
deviationsTsne          deviationsTsne
differentialDeviations
                        differentialDeviations
differentialVariability
                        differentialVariability
example_counts          example_counts
filterPeaks             filterPeaks
filterSamples           filterSamples
filterSamplesPlot       filterSamplesPlot
getAnnotationCorrelation
                        getAnnotationCorrelation
getAnnotationSynergy    getAnnotationSynergy
getAnnotations          getAnnotations
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
mini_counts             mini_counts
mini_dev                mini_dev
mini_ix                 mini_ix
plotDeviationsTsne      plotDeviationsTsne
plotKmerMismatch        plotKmerMismatch
plotVariability         plotVariability
pwmDistance             pwmDistance
rbind,chromVARDeviations-method
                        rbind method chromVARDeviations
readNarrowpeaks         readNarrowpeaks
