AMRverse/AMRgen

AMRgen is an open-source R package designed to support systematic AMR genotype-phenotype analysis. Developed as an extension to the AMR R package, it provides functions to import and harmonise genotypic data from common bioinformatics tools, alongside phenotypic data from automated antimicrobial susceptibility testing (AST) instruments and public repositories, and combine enotype-phenotype data together in a single data structure. AMRgen supports common analyses linking AST data to reference distributions, modelling enotype-phenotype associations, quantifying concordance, and producing publication-ready visualisations including UpSet plots that jointly display genotypic marker combination frequencies and associated phenotypic distributions. This package is developed in collaboration with the ESGEM-AMR Working Group and is tailored for researchers and health professionals tackling AMR globally. The AMRgen website has full function documentation and various vignettes working through analysing geno/pheno data using key functions.

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