Skip to content
@cidgoh

Centre for Infectious Disease and One Health

Hsiao Laboratory at Simon Fraser University

Popular repositories

  1. DataHarmonizer 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 …

    JavaScript 88 23

  2. LexMapr LexMapr Public

    LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms

    Python 20 14

  3. GRDI_AMR_One_Health 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 spreadsh…

    7

  4. ontotrek ontotrek Public

    A 3d ontology visualizer focusing on OBOFoundry.org ontologies

    JavaScript 5

  5. VIRUS-MVP 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 …

    Python 5 2

  6. nf-ncov-voc 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:/…

    Python 4 4

Repositories

Showing 10 of 29 repositories
  • bacpaq Public

    Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data

    Nextflow 2 MIT 2 8 1 Updated Jun 3, 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.

    7 MIT 0 10 0 Updated May 31, 2024
  • pathogen-genomics-package Public

    This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates

    HTML 4 MIT 4 8 1 Updated May 30, 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…

    JavaScript 88 MIT 23 33 3 Updated May 30, 2024
  • 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.

    Python 4 MIT 4 12 (1 issue needs help) 0 Updated May 22, 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.

    Python 5 MIT 2 29 (1 issue needs help) 1 Updated May 10, 2024
  • cidgoh_cloud Public
    HCL 0 0 0 0 Updated May 7, 2024
  • geem Public

    Genomic Epidemiology Entity Mart

    CSS 3 CC-BY-4.0 1 12 2 Updated Apr 17, 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.

    1 1 0 0 Updated Mar 28, 2024
  • pathogen-mutation-functionalannotation-package Public

    Package for functional annotation of mutations

    JavaScript 0 MIT 0 0 0 Updated Mar 23, 2024
View all repositories

Most used topics

Loading…