Antimicrobial resistance prediction app for KBase
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Updated
Aug 29, 2018 - Python
Antimicrobial resistance prediction app for KBase
Analysis and visualisation of antimicrobial resistance
Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike
Detect the presence of specific resistance genes in a sample using the IRIDA system
Nextflow Wrapper for Mykrobe
Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results
Scripts for ARIBA-based gene detection
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
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues
Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"
Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli
PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features
Making whole bacterial genome sequencing data analysis easy
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"
Harmonization of AMR predictor tool outputs
Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi
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