BSFDataSet              BSFDataSet object and constructors
BSFind                  RBP binding site definition for iCLIP data
add-BSFDataSet          Add two 'BSFDataSet' objects
annotateWithScore       Annotation function for BSFDataSet object
assignToGenes           Assign binding sites to their hosting genes
assignToTranscriptRegions
                        Assign binding sites to their hosting
                        transcript regions
bindingSiteCoveragePlot
                        Plot signal coverage of selected ranges
bindingSiteDefinednessPlot
                        Binding site definedness plot
calculateBsBackground   Compute background coverage for binding sites
                        per gene
calculateBsFoldChange   Compute fold-changes per binding site
calculateSignalToFlankScore
                        Calculate signal-to-flank score
clipCoverage            Coverage function for BSFDataSet objects
collapseReplicates      Collapse signal from replicates
combineBSF              Combine multiple 'BSFDataSet' objects
coverageOverRanges      Coverage function for BSFDataSet objects
duplicatedSitesPlot     Plot the number of overlaps when assigning
                        crosslink sites to genes
estimateBsWidth         Function to estimate the appropriate binding
                        site width together with the optimal gene-wise
                        filter level.
estimateBsWidthPlot     Plot the signal-to-flank score for varying
                        gene-wise filter and binding site width
exportTargetGenes       Function to export sorted RBP target genes
exportToBED             Wrapper function to export binding sites as BED
                        files
filterBsBackground      Filter for genes not suitable for differential
                        testing
geneOverlapsPlot        UpSet-plot to that shows the gene type overlaps
geneRegulationPlot      Gene Regulation Plot
getMeta                 Accessor method for the meta data of the
                        BSFDataSet object
getName                 Accessor method for the name of the BSFDataSet
                        object
getRanges               Accessor method for the ranges of the
                        BSFDataSet object
getSignal               Accessor method for the signal data of the
                        BSFDataSet object
getSummary              Accessor method for the summary slot of the
                        BSFDataSet object
globalScorePlot         Plot the PureCLIP score distribution after
                        re-assignment
imputeBsDifferencesForTestdata
                        Impute artificial differences in the example
                        data set
makeBindingSites        Define equally sized binding sites from peak
                        calling results and iCLIP crosslink events.
makeBsSummaryPlot       Plot binding site filter diagnostics
mergeCrosslinkDiagnosticsPlot
                        Plot binding site merging diagnostics
mergeSummaryPlot        Plot summarized results of the different
                        binding site merging and filtering steps
plotBsBackgroundFilter
                        Diagnostic plots for the differential binding
                        background
plotBsMA                MA style plot
plotBsVolcano           Volcano style plot
processingStepsFlowChart
                        Step-wise flowchart plot
processingStepsTable    Create a table of all workflow steps for
                        reporting
pureClipGeneWiseFilter
                        Filter PureCLIP sites by their score
                        distribution per gene
pureClipGlobalFilter    Filter PureCLIP sites by their score
                        distribution
pureClipGlobalFilterPlot
                        Plot the PureCLIP score distribution with
                        global cutoff indicator
quickFigure             Quick figures
rangeCoveragePlot       Plot crosslink event coverage over binding site
                        range
reproducibilityCutoffPlot
                        Plot to that shows how many replicates support
                        each binding site
reproducibilityFilter   Replicate reproducibility filter function
reproducibilityFilterPlot
                        Plot to that shows the crosslink site
                        distribution per replicate
reproducibilitySamplesPlot
                        UpSet-plot to that shows how each replicate
                        supports binding sites
reproducibilityScatterPlot
                        Plot that shows binding site reproducibility as
                        scatter
setMeta                 Setter method for the meta data of the
                        BSFDataSet object
setName                 Setter method for the names of the BSFDataSet
                        object The name slot holds the name information
                        of the dataset
setRanges               Setter method for the ranges of the BSFDataSet
                        object The GRanges object that holds the
                        genomic ranges information can be replaced.
setSignal               Setter method for the signal data of the
                        BSFDataSet object
setSummary              Setter method for the summary slot of the
                        BSFDataSet object
show                    Show method to for the BSFDataSet
subset-BSFDataSet       Subset a BSFDataSet object
summary                 Summary method to for the BSFDataSet
supportRatio            Support ratio function for BSFDataSet objects
supportRatioPlot        Plot that shows the binding site support ratio
targetGeneSpectrumPlot
                        Bar-chart to show the hosting gene types of
                        binding sites
transcriptRegionOverlapsPlot
                        UpSet-plot to that shows the transcript region
                        overlaps
transcriptRegionSpectrumPlot
                        Bar-chart to show the hosting transcript
                        regions of binding sites
