👨💻🧬🤖 deep neural networks: 1Dconvolution experiments with kernel size and stride length
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Updated
Jun 28, 2024 - Jupyter Notebook
👨💻🧬🤖 deep neural networks: 1Dconvolution experiments with kernel size and stride length
Antimicrobial Resistance Test Interpretation Engine
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
AMR/VF LGT focused bacterial genomics analysis workflow
Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow
MTB++ a software developed to predict antimicrobial resistance to 13 antibiotics and 3 families of antimicrobials.
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.
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
Conditional Variational Auto-Encoder for generation of synthetic data for Antimicrobial Resistance.
Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi
Harmonization of AMR predictor tool outputs
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Collection of planning documents, visualizations, and presentations for my dissertation research. "Investigating Multidrug Resistance in Escherichia coli with Phylogenetics and Machine Learning"
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.
Making whole bacterial genome sequencing data analysis easy
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
Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli
HydrAMP: a deep generative model for antimicrobial peptide discovery
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