# Chromatin Variation Across Regions

## Documentation for package ‘chromVAR’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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