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Genomic datasets have grown by orders of magnitude in the last decade and thus require increasingly flexible and streamlined analysis workflows. One major line of research in genomics is gene enrichment analysis, which aims to quantitatively assess whether the genomic basis of a phenotype of interest has higher association with other genomic regions than would be expected by chance. HARE is a Python pipeline which annotates genome-wide significant positions, identifies overlap between these positions and a provided list of genomic features (here called ‘elements’) of interest, and determines enrichment likelihood through a resampling process of random length-matched regions. HARE is written in Python and is available for installation from source or via the Python Package Index (pip).