# Reference

## All functions
`TSSr-class` | TSSr: A package for transcription start site sequencing data analyses.
`TSSr-package` | TSSr: A package for transcription start site sequencing data analyses.
`annotateCluster()` | Annotate clusters with GFF annotation file.
`clusterTSS()` | Cluster TSSs into tag clusters
`consensusCluster()` | Make consensus clusters across multiple samples.
`deGene()` | Analysis of gene differential expression.
`exampleTSSr` `exampleTSSr` | TSSr example data
`exportClustersTable()` | Export cluster tables
`exportClustersToBed()` | Creating bed files of clusters
`exportDETable()` | Export gene differential expression results table
`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.