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@fowler-lab Predicting AMR de novo

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    28 repositories

    • cryptic-catalogues-2025

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Apr 28, 2026Apr 28, 2026

    • gpas-analysis-tools

      Public
      CLI to build CRyPTIC data tables from the outputs of EIT Pathogena
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • catomatic

      Public
      Python code that automatically builds resistance catalogues
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • tb-pnca-gnn

      Public
      graph-based convolutional neural network to predict Pyrazinamide resistance
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Apr 8, 2026Apr 8, 2026

    • ECOFFitter

      Public
      A Python tool to fit an internal regression model to censored Minimum Inhibitory Concentration values.
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 2, 2026Apr 2, 2026

    • sbmlcore

      Public
      Collection of core classes and functions for structure-based machine learning to predict antimicrobial resistance
      Python
      •
      MIT License
      •0•3•3•0•Updated Apr 1, 2026Apr 1, 2026

    • amygda

      Public
      Automated Mycobacterial Growth Detection Algorithm, funded by NIHR Oxford Biomedical Research Centre
      Python
      •
      Other
      •6•1•0•0•Updated Mar 28, 2026Mar 28, 2026

    • validate-myco-amr

      Public
      Data and code to validate the second version of the WHO catalogue of resistance-associated variants in tuberculosis
      Shell
      •
      MIT License
      •1•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • intreg

      Public
      A Python implementation of interval regression
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • sbmlsim

      Public
      Create upsampled/artificial datasets of bacterial alleles for training machine learning models
      Jupyter Notebook
      •
      Other
      •0•0•0•1•Updated Sep 30, 2025Sep 30, 2025

    • predict-rifampicin-resistance

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • tb-rnap-subpopulations

      Public
      Data and code allowing analysis and figures in a manuscript to be reproduced
      Jupyter Notebook
      •
      MIT License
      •0•0•0•1•Updated Sep 2, 2025Sep 2, 2025

    • tb-rnap-compensation

      Public
      Investigation of the role of compensatory mutations in rifamycin resistance in M. tuberculosis
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Jul 25, 2025Jul 25, 2025

    • tb-bdq-cat

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•1•Updated Apr 29, 2025Apr 29, 2025

    • predict-pyrazinamide-resistance

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 6, 2024Mar 6, 2024

    • who_catalogue_conversion

      Public
      Convert mutations from the WHO TB catalogue to GARC
      Python
      •
      Other
      •0•3•0•0•Updated Feb 9, 2024Feb 9, 2024

    • bashthebug

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 29, 2023Oct 29, 2023

    • pyniverse

      Public
      generic Python package for parsing, analysing and plotting Zooniverse data classification export files
      Python
      •
      MIT License
      •1•6•0•0•Updated Oct 29, 2023Oct 29, 2023

    • Protein-Mutation-Viewer

      Public
      HTML
      •1•1•0•3•Updated May 1, 2023May 1, 2023

    • cryptic-ecoffs

      Public
      Data and code to reproduce the figures and tables in the CRyPTIC ECOFF/ECV paper
      Jupyter Notebook
      •
      Other
      •2•1•0•0•Updated Mar 9, 2023Mar 9, 2023

    • molstar-mutation

      Public
      A comprehensive macromolecular library adapted for visualisation of protein mutations
      TypeScript
      •
      MIT License
      •237•0•0•16•Updated Jan 7, 2023Jan 7, 2023

    • tb-rbfe-setup

      Public
      Files and scripts to rerun A90V DNAG and S450L RBFE calculations
      Shell
      •
      MIT License
      •0•0•0•0•Updated Oct 20, 2022Oct 20, 2022

    • bashthebug-consensus-dataset

      Public
      Dataset of classifications made by BashTheBug volunteers used to decide how to form a consensus
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 19, 2022Jul 19, 2022

    • sbmlcore-tutorials

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 22, 2022Jun 22, 2022

    • Inh_resistance

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 25, 2022May 25, 2022

    • tb-lineage-mutations

      Public
      Reference list of lineage-defining mutations as derived from SNP-IT
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 6, 2022Feb 6, 2022

    • jupyter-notebook-example

      Public
      A prototype jupyter notebook
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 10, 2021Oct 10, 2021

    • seqtreat

      Public
      Python code to validate the spreadsheets containing M. tuberculosis AST data donated to the project. Likely to expand in future.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 28, 2020Oct 28, 2020
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