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@cidgoh Centre for Infectious Disease and One Health

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    33 repositories

    • nf-ncov-voc

      Public
      A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
      virusgenomicsnextflowmicrobial-genomicsvariant-callingbioinformaticscovid-19sars-cov-2
      Python
      •
      MIT License
      •5•6•11•1•Updated Nov 12, 2024Nov 12, 2024

    • pathogen-genomics-package

      Public
      This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
      data-harmonizationinfectious-disease
      HTML
      •
      MIT License
      •4•7•8•1•Updated Nov 12, 2024Nov 12, 2024

    • DataHarmonizer

      Public
      A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions…
      javascriptapplicationdataspreadsheetharmonizationlinkmllinkml-schema
      JavaScript
      •
      MIT License
      •27•95•31•3•Updated Nov 12, 2024Nov 12, 2024

    • VIRUS-MVP

      Public
      VirusMVP is an interactive heatmap-centric app that integrates viral genomic mutations, lineage information and curated functional impact to study the spread and evolution of viruses in Canada and globally.
      visualizationbioinformaticsplotlydashcovid-19sars-cov-2
      Python
      •
      MIT License
      •2•6•29•0•Updated Nov 5, 2024Nov 5, 2024

    • bacpaq

      Public
      Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
      bioinformaticsnextflowmicrobial-genomics
      Nextflow
      •
      MIT License
      •3•5•5•0•Updated Oct 9, 2024Oct 9, 2024

    • MPox_Contextual_Data_Specification

      Public
      A data specification for harmonizing MPox pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a the DataHarmonizer, supported by field and reference guides as well as different curation and new term request SOPs.
      0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • Wastewater_Contextual_Data_Specification

      Public
      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.
      MIT License
      •1•2•0•0•Updated Oct 8, 2024Oct 8, 2024

    • HPAI_Contextual_Data_Specification

      Public
      This data specification harmonizes contextual data to support HPAI 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.
      metadatagenomicspathogenontologiesdata-standardsharmonizationavian-influenza
      1•0•0•0•Updated Oct 7, 2024Oct 7, 2024

    • specification-training

      Public
      Training materials about developing and applying data specifications
      0•1•0•0•Updated Sep 10, 2024Sep 10, 2024

    • pathogen-mutation-functionalannotation-package

      Public
      Package for functional annotation of mutations
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • LexMapr

      Public
      LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
      Python
      •
      GNU General Public License v3.0
      •14•21•4•1•Updated Aug 20, 2024Aug 20, 2024

    • GRDI_AMR_One_Health

      Public
      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.
      metadatagenomicspathogenontologiesharmonizationantimicrobial-resistanceone-healthfood-system
      MIT License
      •0•7•5•0•Updated Aug 16, 2024Aug 16, 2024

    • AMBR_Contextual_data_Specification

      Public
      A data specification for harmonizing pathogen genomics contextual data as part ofthe AMBR project. The specification provides standardized (ontology-based) fields and terms which are implemented via a the DataHarmonizer, supported by field and reference guides as well as different curation and new term request SOPs.
      0•0•0•0•Updated Jul 19, 2024Jul 19, 2024

    • CanCOGeN_Contextual_Data_Specification

      Public
      A data specification for harmonizing One Health Canadian COVID pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a the DataHarmonizer, supported by field and reference guides as well as different curation and new term request SOPs.
      metadatagenomicspathogenontologiesharmonizationcovid19-dataone-health
      0•0•3•0•Updated Jul 17, 2024Jul 17, 2024

    • cidgoh_cloud

      Public
      HCL
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • geem

      Public
      Genomic Epidemiology Entity Mart
      CSS
      •
      Creative Commons Attribution 4.0 International
      •1•3•12•2•Updated Apr 17, 2024Apr 17, 2024

    • FastaUploader

      Public
      A tool for batch processing large fasta files and accompanying metadata table to upload to repositories via API
      pythonuploaderfastabatch-processing
      Python
      •
      Creative Commons Zero v1.0 Universal
      •1•1•0•0•Updated Feb 15, 2024Feb 15, 2024

    • ontotraining

      Public
      A repository for ontology training materials
      Creative Commons Zero v1.0 Universal
      •0•2•4•0•Updated Oct 4, 2023Oct 4, 2023

    • training

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • AWS-IRIDA-DEPLOYMENT

      Public
      HCL
      •
      MIT License
      •0•1•0•0•Updated Apr 25, 2023Apr 25, 2023

    • ontotrek

      Public
      A 3d ontology visualizer focusing on OBOFoundry.org ontologies
      JavaScript
      •
      GNU General Public License v3.0
      •0•6•8•0•Updated Jan 24, 2023Jan 24, 2023

    • nf-upcoastv

      Public
      Nextflow
      •
      MIT License
      •2•1•0•0•Updated Jan 17, 2023Jan 17, 2023

    • cidgoh.github.io

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Sep 6, 2022Sep 6, 2022

    • AIV_seeker

      Public
      AIV_seeker is optimized for detecting and identification of Avian Influenza Virus from metagenomics data.
      Python
      •
      MIT License
      •5•1•0•0•Updated Aug 11, 2022Aug 11, 2022

    • covidmvp_deployment

      Public
      Deployment of covid map app using docker
      HTML
      •3•0•0•0•Updated May 9, 2022May 9, 2022

    • MISO_LIMS_Cloud

      Public
      HCL
      •
      MIT License
      •0•0•0•0•Updated Apr 28, 2022Apr 28, 2022

    • CC_data_manager

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 26, 2022Apr 26, 2022

    • cidgoh_ip_monitor

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 31, 2022Mar 31, 2022

    • cidgoh_qc

      Public
      Workflow for quality check for NGS data
      Nextflow
      •
      MIT License
      •3•0•0•0•Updated Feb 17, 2022Feb 17, 2022

    • datatype_mapper

      Public
      An application that provides a suite of field datatype parsing and mapping expressions. It aims to achieve bi-directional data exchange.
      JavaScript
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Mar 15, 2021Mar 15, 2021