Antimicrobial Resistance Python Packages

maldiamrkit

Comprehensive toolkit for MALDI-TOF mass spectrometry data preprocessing for antimicrobial resistance (AMR) prediction purposes

dna-decode

Deterministic, interpretable genome→phenotype decoder: calls antibiotic/antiviral/antifungal resistance from DNA + names the exact genes/mutations driving each call. Spans bacteria, M. tuberculosis, fungi, HIV-1 & SARS-CoV-2 — independently validated on FREE measured wet-lab labels (EBI AMR Portal, Stanford HIVDB). Not a clinical tool.

gnomonicus

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

respredai

Implementation of the pipeline described in the work "Artificial intelligence model to predict resistances in Gram-negative bloodstream infections" by Bonazzetti et al., npj Digit. Med. 8, 319 (2025)

staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

hamronization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

maldideepkit

Catalog of sklearn-compatible deep learning classifiers for MALDI-TOF binned spectra

maldibatchkit

Batch-effect correction methods for MALDI-TOF spectra in clinical AMR prediction workflows

maldisuite

MaldiSuite - a Python ecosystem for MALDI-TOF spectral processing and analysis in antimicrobial resistance research

staphscope-typing-tool

Staphscope Typing Tool — MLST + spa + SCCmec typing for Staphylococcus aureus