https://github.com/interpretamr/amrgen
The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimicrobial susceptibility testing (AST) data, and calculating genotype-phenotype associations.
https://github.com/interpretamr/amrgen
eucast genotyping phenotyping r
Last synced: 5 months ago
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The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimicrobial susceptibility testing (AST) data, and calculating genotype-phenotype associations.
- Host: GitHub
- URL: https://github.com/interpretamr/amrgen
- Owner: interpretAMR
- License: gpl-3.0
- Created: 2024-11-29T11:00:33.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2024-12-24T15:29:49.000Z (5 months ago)
- Last Synced: 2025-01-02T12:14:02.686Z (5 months ago)
- Topics: eucast, genotyping, phenotyping, r
- Language: R
- Homepage: https://interpretAMR.github.io/AMRgen/
- Size: 1.29 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# AMRgen
R Package for Genetic and Phenotypic Resistance Interpretation
## Overview
**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](https://github.com/msberends/AMR), 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.
------------------------------------------------------------------------
## Key Features
> 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](https://mic.eucast.org) 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.
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## Getting Started
To install and explore the package, follow the instructions below:
### Installation
``` r
# Install from GitHub
remotes::install_github("interpretAMR/AMRgen")
```
## Usage Examples
_Will follow shortly_
## Contributions
Contributions are welcome! If you encounter issues or wish to suggest new features, please open an issue or submit a pull request.
## Licence
This package is distributed under the GNU GPL-3.0 Licence. See `LICENSE` for details.