CAGEr-package           Analysis of CAGE (Cap Analysis of Gene
                        Expression) sequencing data for precise mapping
                        of transcription start sites and promoterome
                        mining
CAGEset-class           Class '"CAGEset"'
CTSSclusteringMethod    Extracting CTSS clustering method from CAGEset
                        object
CTSScoordinates         Extracting genomic coordinates of TSSs from
                        CAGEset object
CTSSnormalizedTpm       Extracting normalized CAGE signal for TSSs from
                        CAGEset object
CTSStagCount            Extracting CAGE tag count for TSSs from CAGEset
                        object
aggregateTagClusters    Aggregating tag clusters across multiple CAGE
                        datasets
clusterCTSS             Clustering CTSSs into tag clusters (TCs)
consensusClusters       Extracting consensus clusters from CAGEset
                        object
consensusClustersTpm    Extracting consensus clusters tpm matrix from
                        CAGEset object
cumulativeCTSSdistribution
                        Calculating cumulative sum of CAGE signal along
                        genomic region
exampleCAGEset          Example CAGEset object with zebrafish CAGE data
exportCTSStoBedGraph    Creating bedGraph tracks of CAGE transcription
                        starts sites
exportToBed             Creating BED tracks of TSSs and clusters of
                        TSSs
expressionClasses       Extracting labels of expression classes
extractExpressionClass
                        Extracting elements of the specified expression
                        class
genomeName              Extracting genome name from CAGEset object
getCTSS                 Reading CAGE data from input file(s) and
                        detecting TSSs
getExpressionProfiles   CAGE data based expression clustering
getShiftingPromoters    Selecting consensus clusters with shifting
                        score above specified threshold
importPublicData        Importing publicly available CAGE data from R
                        data packages
inputFiles              Extracting paths to input files from CAGEset
                        object
inputFilesType          Extracting type of input files from CAGEset
                        object
librarySizes            Extracting library sizes from CAGEset object
mergeSamples            Merging CAGE datasets (samples)
normalizeTagCount       Normalizing raw CAGE tag count
plotCorrelation         Plotting pairwise scatter plots of CAGE signal
                        and calculating correlation between samples
plotExpressionProfiles
                        Plotting expression profiles derived from CAGE
                        data
plotInterquantileWidth
                        Plotting distribution of interquantile width
plotReverseCumulatives
                        Plotting reverse cumulative number of CAGE tags
                        per CTSS
quantilePositions       Determining positions of CAGE signal quantiles
                        within genomic region
sampleLabels            Extracting CAGE datasets labels from CAGEset
                        object
scoreShift              Calculating promoter shifting score
setColors               Setting colors for samples
show-methods            Methods for function 'show'
tagClusters             Extracting tag clusters (TCs) for individual
                        CAGE experiment from CAGEset object
