Amr Python Packages

penman

PENMAN notation (e.g. AMR) in Python

amr

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

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.

amrlib

A python library that makes AMR parsing, generation and visualization simple.

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)

amr-logic-converter

Convert Abstract Meaning Representation (AMR) into first-order logic

peclet-core

Shared infrastructure for the Peclet suite: MPI block decomposition, async ghost-layer exchange, SDF geometry, dynamic load balancing, AMR octree (header-only C++20 + Kokkos)

perin-parser

PERIN is Permutation-Invariant Semantic Parser developed for MRP 2020

zensols-amr

AMR annotation and feature generation

smatchpp

A Python package for graph processing

maldideepkit

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

bacant

This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria

amira-amr

A tool to detect acquired AMR genes directly from long read sequencing data.

transition-neural-parser

SoTA Abstract Meaning Representation (AMR) parsing with word-node alignments in Pytorch. Includes checkpoints and other tools such as statistical significance Smatch.

maldibatchkit

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

iec62056-21

A Python library for IEC62056-21, Local Data Readout of Energy Meters. Former IEC1107

unofficial-stog

AMR Parsing as Sequence-to-Graph Transduction

splitfdm

1D Finite-Difference with AMR and steady-state solver using Newton and Split-Newton

splitfvm

1D Finite-Volume Split Newton Solver

maldisuite

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

ndtamr

N-dimensional adaptive mesh refinement tree structure in Python.

zensols-clinicamr

Clincial Domain Abstract Meaning Representation Graphs

iec62056-21-dzg

A Python library for IEC62056-21, Local Data Readout of Energy Meters, specialy DZG. Former IEC1107