Chromatin Variation Across Regions


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Documentation for package ‘chromVAR’ version 1.31.0

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