Scripts for ARIBA-based gene detection
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Updated
Jul 20, 2022 - Python
Scripts for ARIBA-based gene detection
Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike
Antimicrobial resistance prediction app for KBase
Detect the presence of specific resistance genes in a sample using the IRIDA system
Conditional Variational Auto-Encoder for generation of synthetic data for Antimicrobial Resistance.
Analysis and visualisation of antimicrobial resistance
Nextflow Wrapper for Mykrobe
Software supporting M. Cavallaro, et al., Informing antimicrobial stewardship with explainable AI. PLOS Digit Health 2(1): e0000162 (2023) https://doi.org/10.1371/journal.pdig.0000162
AMRFinderPlus-Matrix contains script for processing the output files of AMRFinderPlus and generating a binary matrix that shows the presence or absence of antibiotic resistance genes, stress response genes, and virulence genes in each sample.
Collection of planning documents, visualizations, and presentations for my dissertation research. "Investigating Multidrug Resistance in Escherichia coli with Phylogenetics and Machine Learning"
Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli
Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results
A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues
👨💻🧬🤖 deep neural networks: 1Dconvolution experiments with kernel size and stride length
MTB++ a software developed to predict antimicrobial resistance to 13 antibiotics and 3 families of antimicrobials.
Antimicrobial Resistance Test Interpretation Engine
Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi
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