Antimicrobial Resistance Python Packages

maldiamrkit

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

amr-clonalshare

Lineage structure in antimicrobial susceptibility tables: the lineage share of calls and of the recorded MIC ordering, and the lineage share of the unobserved MIC ordering that censored readings guarantee, with valid confidence limits.

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)

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.

mobiorigin

MobiOrigin classifies bacterial contigs as plasmid, chromosome, phage, or unclassified using sequence, coding and mobility-marker evidence.

maldideepkit

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

staramr

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

hamronization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

maldisuite

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

mic-50-90

MIC-50-90: MIC distribution bounds from incomplete reports, guided Windows and CLI analysis, and verifiable laboratory reporting.

maldibatchkit

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

staphscope

StaphScope is a comprehensive bioinformatics tool for Staphylococcus aureus genomic analysis including MLST typing, spa typing, SCCmec analysis, antimicrobial resistance detection, virulence factors, plasmid profiling, and lineage prediction from whole genome sequencing data. Designed specifically for MRSA research

staphscope-typing-tool

StaphScope is a comprehensive bioinformatics tool for Staphylococcus aureus genomic analysis including MLST typing, spa typing, SCCmec analysis, antimicrobial resistance detection, virulence factors, plasmid profiling, and lineage prediction from whole genome sequencing data. Designed specifically for MRSA research