TSSr-accessors          Access data stored in a TSSr object
TSSr-class              TSSr: A package for transcription start site
                        sequencing data analyses.
annotateCluster         Annotate clusters with GFF annotation file.
callEnhancer            Identification of enhancers
clusterTSS              Cluster TSSs into tag clusters
consensusCluster        Make consensus clusters across multiple
                        samples.
deGene                  Analysis of gene differential expression.
exampleTSSr             TSSr example data
exportClustersTable     Export cluster tables
exportClustersToBed     Creating bed files of clusters
exportDETable           Export gene differential expression results
                        table
exportEnhancerTable     Export enhancer tables
exportShapeTable        Export core promoter shape score tables
exportShiftTable        Export core promoter shift table
exportTSStable          Export TSS tables
exportTSStoBedgraph     Creating Bedgraph/BigWig tracks of TSSs
filterTSS               Filter raw TSS counts or normalized TSS
getTSS                  Precisely identify TSSs from bam files, paired
                        end bam files, bed files, BigWig files, tss
                        files, or tss tables.
mergeSamples            Merge TSS samples
normalizeTSS            Normalize raw TSS counts
plotCorrelation         Pairwise scatter plots and correlations of TSS
                        signal
plotDE                  Plot gene differential expressions
plotInterQuantile       Plot core promoter interquantile width
plotShape               Plot core promoter shape
plotTSS                 Plot TSSs and clusters
plotTssPCA              Plotting principle component analysis (PCA)
shapeCluster            Analysis of core promoter shape
shiftPromoter           Select genes which have core promoter shift
                        across different experiments.
show,TSSr-method        Display a compact summary of a TSSr object
