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 |