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Provides a comprehensive toolbox for analysis and visualization of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites (TSS) and promoterome mining in R. CAGEr performs identification of transcription start sites and frequency of their usage from input CAGE sequencing data, normalization of raw CAGE tag count, clustering of TSSs into tag clusters (TC) and their aggregation across multiple CAGE experiments to construct the promoterome. It manipulates multiple CAGE experiments at once, performs expression profiling across experiments both at level of individual TSSs and clusters of TSSs and exports several different types of track files for visualization in the genome browser.