Pinned Repositories
contextual_data_QC_tags
Standardized attributes for labelling sequence datasets with known quality control issues
hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
hAMRonization_workflow
Harmonization of AMR predictor tool outputs
pha4ge.github.io
Static website for the PH4AGE alliance
pipeline-resources
Bioinformatics Pipeline and Visualization resources
primer-schemes
Tiling PCR primer scheme definitions
public-health-pipeline-best-practices
SARS-CoV-2-Contextual-Data-Specification
Collection template and associated materials for SARS-CoV-2 metadata
wastewater-guidance
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's Repositories
pha4ge/hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
pha4ge/pipeline-resources
Bioinformatics Pipeline and Visualization resources
pha4ge/SARS-CoV-2-Contextual-Data-Specification
Collection template and associated materials for SARS-CoV-2 metadata
pha4ge/hAMRonization_workflow
Harmonization of AMR predictor tool outputs
pha4ge/public-health-pipeline-best-practices
pha4ge/pha4ge.github.io
Static website for the PH4AGE alliance
pha4ge/primer-schemes
Tiling PCR primer scheme definitions
pha4ge/contextual_data_QC_tags
Standardized attributes for labelling sequence datasets with known quality control issues
pha4ge/wastewater-guidance
pha4ge/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/minimal-pathogen-agnostic-contextual-data-specification
An international minimal metadata standard for public health and One Health genomic surveillance.
pha4ge/training-resources
Training and workforce development resources
pha4ge/convAST
pha4ge/infrastructure-resources
Infrastructure resources
pha4ge/primaschema
Infrastructure for tiled amplicon PCR primer scheme definitions
pha4ge/SARS-CoV-2-Data-Spec-JSON
PHA4GE's SARS-CoV-2 Data Specification Processing Tool
pha4ge/HPAI_Contextual_Data_Specification
This data specification harmonizes contextual data to support H5N1 monitoring with PHA4GE. It provides standardized, ontology-based fields and terms for comprehensive surveillance. Users can implement it via their preferred tools, including DataHarmonizer. Field and reference guides, along with curation and new term request SOPs, support its use.
pha4ge/varnish
Template for pkgdown site