API for ZarnackGroup/BindingSiteFinder
Binding site defintion based on iCLIP data
| Global functions | |
|---|---|
| +,BSFDataSet,BSFDataSet-method | Man page |
| .approximateBindingSites_coarse | Source code |
| .approximateBindingSites_medium | Source code |
| .calcNormalizeFactors | Source code |
| .capitalize | Source code |
| .checkForDropSeqlevels | Source code |
| .collapseSamples | Source code |
| .computeSupportRatio | Source code |
| .coverageOverRanges.merge_all_replicates | Source code |
| .coverageOverRanges.merge_positions_keep_replicates | Source code |
| .coverageOverRanges.merge_ranges_keep_positions | Source code |
| .coverageOverRanges.merge_replicates_per_condition | Source code |
| .filterCenterClSite | Source code |
| .filterCenterSummit | Source code |
| .filterMinClSites | Source code |
| .filterMinCrosslinks | Source code |
| .findFirstMaximum | Source code |
| .findFirstMaximum_local | Source code |
| .makeCoverageMatrix | Source code |
| .makeCoverageVector | Source code |
| .matchMetaData | Source code |
| .mergeCrosslinkSites | Source code |
| .mergePositions | Source code |
| .mergeRanges | Source code |
| .mergeSamples | Source code |
| .pairsCorColor | Source code |
| .pairsDensity | Source code |
| .parisCorrelationPlot | Source code |
| .reduceSignalToFrame | Source code |
| .resolveGeneOverlapsWithRule | Source code |
| .selectQuantilesMultipleConditions | Source code |
| .selectQuantilesSingleCondtion | Source code |
| .sortRanges | Source code |
| .subsetByChr | Source code |
| .subsetByChr_old | Source code |
| BSFDataSet | Man page Source code |
| BSFDataSet, | Man page |
| BSFDataSet-class, | Man page |
| BSFDataSetFromBigWig | Man page Source code |
| BSFind | Man page Source code |
| [,BSFDataSet,ANY,ANY,ANY-method | Man page |
| add-BSFDataSet | Man page |
| annotateWithScore | Man page Source code |
| assignToGenes | Man page Source code |
| assignToTranscriptRegions | Man page |
| bindingSiteCoveragePlot | Man page Source code |
| bindingSiteDefinednessPlot | Man page Source code |
| calculateBsBackground | Man page Source code |
| calculateBsFoldChange | Man page |
| calculateSignalToFlankScore | Man page Source code |
| clipCoverage | Man page Source code |
| collapseReplicates | Man page Source code |
| combineBSF | Man page Source code |
| coverageOverRanges | Man page Source code |
| duplicatedSitesPlot | Man page Source code |
| estimateBsWidth | Man page |
| estimateBsWidthPlot | Man page Source code |
| exportTargetGenes | Man page Source code |
| exportToBED | Man page Source code |
| filterBsBackground | Man page |
| geneOverlapsPlot | Man page Source code |
| geneRegulationPlot | Man page Source code |
| getMeta | Man page |
| getMeta,BSFDataSet-method | Man page |
| getName | Man page |
| getName,BSFDataSet-method | Man page |
| getRanges | Man page |
| getRanges,BSFDataSet-method | Man page |
| getSignal | Man page |
| getSignal,BSFDataSet-method | Man page |
| getSummary | Man page |
| getSummary,BSFDataSet-method | Man page |
| globalScorePlot | Man page Source code |
| imputeBsDifferencesForTestdata | Man page |
| makeBindingSites | Man page Source code |
| makeBsSummaryPlot | Man page Source code |
| mergeCrosslinkDiagnosticsPlot | Man page Source code |
| mergeSummaryPlot | Man page Source code |
| plotBsBackgroundFilter | Man page Source code |
| plotBsMA | Man page Source code |
| plotBsVolcano | Man page Source code |
| processingStepsFlowChart | Man page Source code |
| processingStepsTable | Man page Source code |
| pureClipGeneWiseFilter | Man page Source code |
| pureClipGlobalFilter | Man page Source code |
| pureClipGlobalFilterPlot | Man page Source code |
| quickFigure | Man page Source code |
| rangeCoveragePlot | Man page Source code |
| reproducibilityCutoffPlot | Man page Source code |
| reproducibilityFilter | Man page Source code |
| reproducibilityFilterPlot | Man page Source code |
| reproducibilitySamplesPlot | Man page Source code |
| reproducibilityScatterPlot | Man page Source code |
| setMeta | Man page |
| setMeta,BSFDataSet-method | Man page |
| setName | Man page |
| setName,BSFDataSet-method | Man page |
| setRanges | Man page |
| setRanges,BSFDataSet-method | Man page |
| setSignal | Man page |
| setSignal,BSFDataSet-method | Man page |
| setSummary | Man page |
| setSummary,BSFDataSet-method | Man page |
| show | Man page |
| show,BSFDataSet-method | Man page |
| subset-BSFDataSet | Man page |
| summary | Man page |
| summary,BSFDataSet-method | Man page |
| supportRatio | Man page Source code |
| supportRatioPlot | Man page Source code |
| targetGeneSpectrumPlot | Man page Source code |
| transcriptRegionOverlapsPlot | Man page Source code |
| transcriptRegionSpectrumPlot | Man page Source code |
