assignGeneID            Annotate ranges with gene ID.
assignMissingID         Annotate ranges with missing IDs.
assignTxID              Annotate ranges with transcript ID.
assignTxType            Annotate ranges with transcript type.
balanceBC               Balance statistic: Bhattacharyya coefficient
                        (BC)
balanceD                Balance statistic: Andersson's D.
bwCommonGenome          Find a common genome for a series of BigWig
                        files.
bwGenomeCompatibility   Check if BigWig-files are compatible with a
                        given genome.
bwValid                 Check if BigWig-files are valid.
calcBidirectionality    Calculate sample-wise bidirectionally of
                        clusters.
calcComposition         Calculate composition of CAGE data.
calcPooled              Calculate pooled expression across all samples.
calcShape               Calculate Tag Cluster shapes
calcSupport             Calculate support of CAGE data.
calcTPM                 Calculate CAGE Tags-Per-Million (TPM)
calcTotalTags           Calculate the total number of CAGE tags across
                        samples.
checkCTSSs              Helper for checking files containing CTSSs
checkPeaked             Helper for checking cluster with peaks
checkPooled             Helper for checking pooled signal
clusterBidirectionally
                        Bidirectional clustering of pooled CTSSs.
clusterUnidirectionally
                        Unidirectional Clustering (Tag Clustering) of
                        pooled CTSSs.
combineClusters         Combine two CAGE experiments.
convertBAM2BigWig       Extract CTSSs from BAM-files (EXPERIMENTAL)
convertBED2BigWig       Convert CTSSs stored in different file formats.
convertGRanges2GPos     Convert GRanges with scores to GPos
exampleDesign           Example CAGE Data
findLinks               Find nearby pairs of clusters and calculate
                        pairwise correlations.
findStretches           Find stretches of clusters
quantifyCTSSs           Quantify CAGE Transcriptions Start Sites
                        (CTSSs)
quantifyCTSSs2          Quantify CAGE Transcriptions Start Sites
                        (CTSSs)
quantifyClusters        Quantify expression of clusters (TSSs or
                        enhancers) by summing CTSSs within clusters.
quantifyGenes           Quantify expression of genes
quickEnhancers          Identify and quantify enhancers.
quickGenes              Identify and quantify genes.
quickTSSs               Identify and quantify Transcription Start Sites
                        (TSSs).
shapeEntropy            Shape statistic: Shannon Entropy
shapeIQR                Shape statitic: Interquartile range
shapeMean               Shape statistic: Mean
shapeMultimodality      Shape statistic: Multimodality
subsetByBidirectionality
                        Subset by sample-wise bidirectionality of
                        clusters.
subsetByComposition     Subset by composition across samples
subsetBySupport         Subset by support across samples
swapRanges              Swap ranges in a GRanges.
swapScores              Swap scores in SummarizedExperiment
trackBalance            Create Genome Browser Track of bidirectional
                        balance scores
trackCTSS               Create Genome Browser track of CTSSs.
trackClusters           Create genome browser track of clusters.
trackLinks              Create a genome browser track of links.
trimToPeak              Trim width of TCs by distance from TC peak
trimToPercentiles       Trim width of TCs to expression percentiles
tuneTagClustering       Determine the optimal pooled threshold for
                        unidirectional tag clustering.
utilsAggregateRows      Utility: Aggregate rows
utilsDeStrand           Utility: Split Genomic Ranges by strand
utilsScoreOverlaps      Utility: Counting overlaps taking into account
                        scores
utilsSimplifyTxDb       Utility: Extract annotation hierachy from a
                        TxDb.
