Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike
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Updated
Apr 3, 2020 - Clojure
Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike
Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli
Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
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"
Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi
A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues
Conditional Variational Auto-Encoder for generation of synthetic data for Antimicrobial Resistance.
Analysis and visualisation of antimicrobial resistance
Nextflow Wrapper for Mykrobe
Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow
MTB++ a software developed to predict antimicrobial resistance to 13 antibiotics and 3 families of antimicrobials.
👨💻🧬🤖 deep neural networks: 1Dconvolution experiments with kernel size and stride length
A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
Scripts for ARIBA-based gene detection
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