R Package for Genetic and Phenotypic Resistance Interpretation
AMRgen is an open-source R package designed to bridge the gap between genotypic and phenotypic antimicrobial resistance (AMR) data. Developed as an extension to the AMR R package, it provides tools to interpret AMR genes, integrate these findings with antimicrobial susceptibility test (AST) data, and calculate genotype-phenotype associations.
This package is developed in collaboration with the ESGEM-AMR Working Group and is tailored for researchers and healthcare professionals tackling AMR globally.
NOTE: These features are intended to develop in the near future
- Genotype-Phenotype Integration: Links AMR gene presence with phenotypic resistance profiles, enabling deeper insights into resistance mechanisms.
- Automated EUCAST MIC Distribution Integration: Fetch MIC distribution data directly from EUCAST for seamless comparison with local susceptibility data.
- Visualisation: Generate powerful UpSet plots to identify intersections of AMR gene presence and phenotypic resistance, highlighting multidrug resistance patterns.
- NCBI-Compliant Export: Create NCBI-compliant antibiograms for global data sharing and interoperability with surveillance platforms.
- Modular and Extensible: Leverages the robust foundation of the AMR package, including antibiotic selectors and clinical breakpoint interpretations.
To install and explore the package, follow the instructions below:
# Install from GitHub
remotes::install_github("interpretAMR/AMRgen")Will follow shortly
Contributions are welcome! If you encounter issues or wish to suggest new features, please open an issue or submit a pull request.
This package is distributed under the GNU GPL-3.0 Licence. See LICENSE for details.