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DebarcodeR is a pipeline for demultiplexing florescence cell barcoded (FCB) flow cytometery datasets. It takes one or more barcoded FCS files as an input and provides a set of debarcoded FCS files - one for each sample + one for unassigned cells, as an output. It is designed to fit into any standard flowCore workflow, starting with flowFrames or flowSets which have been appropriately compensated, transformed, and gated.