.byCtss                 Apply functions to identical CTSSes.
.clusterAggregateAndSum
                        Aggregate identical clusters and sum their
                        scores.
.get.quant.pos          Get quantile positions
.powerLaw               .powerLaw
CAGEexp-class           CAGEr class to hold all data and metadata about
                        one CAGE experiment.
CAGEr-class             CAGEr objects
CAGEr-package           Analysis of CAGE (Cap Analysis of Gene
                        Expression) sequencing data for precise mapping
                        of transcription start sites and promoterome
                        mining
CAGEr_Multicore         Multicore support in CAGEr
CAGEset-class           Class '"CAGEset"'
CTSS-class              Classes for type safety.
CTSSclusteringMethod    Get /set CTSS clustering method
CTSScoordinates         Genomic coordinates of TSSs from a 'CAGEr'
                        object
CTSScumulativesTagClusters
                        Get/set CTSS cumulative TC or CC data
CTSSnormalizedTpm       Extracting normalized CAGE signal for TSSs from
                        CAGEr objects
CTSStagCount            Extract raw CAGE TSSs expression tables from
                        'CAGEr' objects
CTSStagCountTable       Extracting CAGE tag count for TSSs from CAGEr
                        objects
CTSStoGenes             Make a gene expression table.
CustomConsensusClusters
                        Expression levels of consensus cluster
FANTOM5humanSamples     List of FANTOM5 human CAGE samples
FANTOM5mouseSamples     List of FANTOM5 mouse CAGE samples
GeneExpDESeq2           Export gene expression data for DESeq2 analysis
GeneExpSE               Retreives the SummarizedExperiment containing
                        gene expression levels.
Strand invaders         Detect and remove strand invasion artefacts
aggregateTagClusters    Aggregate TCs across all samples
annotateCTSS            Annotate and compute summary statistics
bam2CTSS                bam2CTSS
clusterCTSS             Cluster CTSSs into tag clusters
coerceInBSgenome        coerceInBSgenome
consensusClusterConvertors
                        Private functions to convert CC formats
consensusClusters<-     Set consensus clusters from CAGEr objects
consensusClustersDESeq2
                        Export _consensus cluster_ expression data for
                        DESeq2 analysis
consensusClustersGR     Get consensus clusters from CAGEr objects
consensusClustersQuantile
                        Quantile metadata stored in CAGEr objects.
consensusClustersTpm    Extracting consensus clusters tpm matrix from
                        CAGEset object
coverage-functions      Private functions behind
                        'cumulativeCTSSdistribution'
cumulativeCTSSdistribution
                        Cumulative sums of CAGE counts along genomic
                        regions
distclu-functions       Private functions for distance clustering.
exampleCAGEexp          Example CAGEexp object.
exampleCAGEset          Example CAGEset object with zebrafish CAGE data
exampleZv9_annot        Example zebrafish annotation data
exportCTSStoBedGraph    Creating bedGraph/bigWig tracks of CAGE
                        transcription starts sites
exportToBed             Create BED tracks of TSSs and clusters of TSSs
expressionClasses       Extract labels of expression classes
extractExpressionClass
                        Extract elements of the specified expression
                        class
genomeName              Extracting genome name from CAGEr objects
getCTSS                 Reading CAGE data from input file(s) and
                        detecting TSSs
getExpressionProfiles   CAGE data based expression clustering
getShiftingPromoters    Select consensus clusters with shifting score
                        above threshold
hanabi                  Calcultate richness in preparation for plotting
hanabi-class            Hanabi class
hanabiPlot              hanabiPlot
import.CAGEscanMolecule
                        import.CAGEscanMolecule
import.CTSS             import.CTSS
import.bam              import.bam
import.bam.ctss         import.bam.ctss
import.bedCTSS          import.bedCTSS
import.bedScore         import.bedScore
import.bedmolecule      import.bedmolecule
importPublicData        Importing publicly available CAGE data from
                        various resources
inputFiles              Extracting paths to input files from CAGEr
                        objects
inputFilesType          Input file formats for CAGEr objects
librarySizes            Extracting library sizes from CAGEr objects
loadFileIntoGPos        loadFileIntoGPos
mapStats                Process mapping statistics
mapStatsScopes          mapStats scopes
mergeCAGEsets           Merge two CAGEr objects into one
mergeSamples            Merge CAGE samples
moleculesGR2CTSS        moleculesGR2CTSS
normalizeTagCount       Normalizing raw CAGE tag count
parseCAGEscanBlocksToGrangeTSS
                        parseCAGEscanBlocksToGrangeTSS
plot.hanabi             Plotting Hanabi objects
plotAnnot               Plot annotation statistics
plotCorrelation         Pairwise scatter plots and correlations of CAGE
                        signal
plotExpressionProfiles
                        Plotting expression profiles derived from CAGE
                        data
plotInterquantileWidth
                        Plot cluster widths
plotReverseCumulatives
                        Plot reverse cumulative number of CAGE tags per
                        CTSS
quantilePositions       Determine CTSS quantile positions within
                        clusters
ranges2annot            Hierarchical annotation of CTSSes
ranges2genes            ranges2genes
ranges2names            ranges2names
sampleLabels            Get and set sample labels
scoreShift              Calculate promoter shifting score
seqNameTotalsSE         Retreives the SummarizedExperiment containing
                        chromosome expression totals.
setColors               Set colors for samples
show-methods            Methods for function 'show'
summariseChrExpr        Expression levels by chromosomes
tagClusterConvertors    Private functions to convert TC formats
tagClusters             Extract tag clusters (TCs) for individual CAGE
                        experiments
tagClustersQuantile     Quantile metadata stored in CAGEr objects.
