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Public Health Alliance for Genomic Epidemiology

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  1. hAMRonization hAMRonization Public

    Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

    Python 173 34

  2. pipeline-resources pipeline-resources Public

    Bioinformatics Pipeline and Visualization resources

    60 35

  3. sars-cov-2-contextual-data-specification sars-cov-2-contextual-data-specification Public

    Collection template and associated materials for SARS-CoV-2 metadata

    37 9

  4. hAMRonization-workflow hAMRonization-workflow Public

    Harmonization of AMR predictor tool outputs

    Python 26 9

  5. public-health-pipeline-best-practices public-health-pipeline-best-practices Public

    17 4

  6. pha4ge.github.io pha4ge.github.io Public

    Static website for the PH4AGE alliance

    13 2

Repositories

Showing 10 of 20 repositories
  • training-resources Public

    Training and workforce development resources

    pha4ge/training-resources’s past year of commit activity
    HTML 5 Apache-2.0 10 0 0 Updated Jan 13, 2026
  • primaschema Public Forked from bede/primaschema

    Infrastructure for tiled amplicon PCR primer scheme definitions

    pha4ge/primaschema’s past year of commit activity
    Python 1 MIT 5 17 0 Updated Jan 9, 2026
  • hAMRonization Public

    Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

    pha4ge/hAMRonization’s past year of commit activity
    Python 173 LGPL-3.0 34 4 (1 issue needs help) 1 Updated Nov 27, 2025
  • GenEpi-Network-DSDI Public

    Data Standards and Data Integration Working Group

    pha4ge/GenEpi-Network-DSDI’s past year of commit activity
    0 0 0 0 Updated Nov 10, 2025
  • wastewater-guidance Public
    pha4ge/wastewater-guidance’s past year of commit activity
    9 Apache-2.0 2 1 0 Updated Nov 6, 2025
  • genotyping-specification Public

    A data specification for harmonizing microbial typing contextual data. The specification provides standardized (ontology-based) fields and terms which can be implemented in tooling, with supporting guidance.

    pha4ge/genotyping-specification’s past year of commit activity
    1 MIT 0 0 0 Updated Oct 1, 2025
  • infrastructure-resources Public

    Infrastructure resources

    pha4ge/infrastructure-resources’s past year of commit activity
    4 Apache-2.0 1 1 0 Updated Aug 24, 2025
  • wastewater-contextual-data-specification Public Forked from cidgoh/Wastewater_Contextual_Data_Specification

    A data specification for harmonizing Wastewater pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via metadata template(s), supported by field and reference guides as well as different curation and new term request SOPs.

    pha4ge/wastewater-contextual-data-specification’s past year of commit activity
    7 MIT 1 5 0 Updated Mar 4, 2025
  • varnish Public Forked from carpentries/varnish

    Template for pkgdown site

    pha4ge/varnish’s past year of commit activity
    SCSS 0 53 0 0 Updated Feb 27, 2025
  • hAMRonization-workflow Public

    Harmonization of AMR predictor tool outputs

    pha4ge/hAMRonization-workflow’s past year of commit activity
    Python 26 9 4 0 Updated Jan 14, 2025
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