Chromatin Variation Across Regions
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Documentation for package ‘chromVAR’ version 1.31.0
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 |