Pinned Repositories
bacpaq
Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
DataHarmonizer
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 from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
geem
Genomic Epidemiology Entity Mart
GRDI_AMR_One_Health
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.
LexMapr
LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
nf-ncov-voc
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.
ontotraining
A repository for ontology training materials
ontotrek
A 3d ontology visualizer focusing on OBOFoundry.org ontologies
pathogen-genomics-package
This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
VIRUS-MVP
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.
Centre for Infectious Disease and One Health's Repositories
cidgoh/DataHarmonizer
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 from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
cidgoh/LexMapr
LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
cidgoh/GRDI_AMR_One_Health
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.
cidgoh/pathogen-genomics-package
This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
cidgoh/VIRUS-MVP
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.
cidgoh/ontotrek
A 3d ontology visualizer focusing on OBOFoundry.org ontologies
cidgoh/nf-ncov-voc
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.
cidgoh/geem
Genomic Epidemiology Entity Mart
cidgoh/bacpaq
Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
cidgoh/ffp_phylogeny
A Galaxy tool for calculating Feature Frequency Profiles (FFP) from fasta sequence and text data.
cidgoh/ontotraining
A repository for ontology training materials
cidgoh/AIV_seeker
AIV_seeker is optimized for detecting and identification of Avian Influenza Virus from metagenomics data.
cidgoh/AWS-IRIDA-DEPLOYMENT
cidgoh/FastaUploader
A tool for batch processing large fasta files and accompanying metadata table to upload to repositories via API
cidgoh/nf-upcoastv
cidgoh/rcqc
Report Calc for Quality Control is a python command line and Galaxy bioinformatics platform tool for text-mining log and data files to create reports and even to stop workflow execution in response to critical quality control issues.
cidgoh/specification-training
Training materials about developing and applying data specifications
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.
cidgoh/CC_data_manager
cidgoh/cidgoh.github.io
cidgoh/cidgoh_cloud
cidgoh/cidgoh_ip_monitor
cidgoh/cidgoh_qc
Workflow for quality check for NGS data
cidgoh/covidmvp_deployment
Deployment of covid map app using docker
cidgoh/datatype_mapper
An application that provides a suite of field datatype parsing and mapping expressions. It aims to achieve bi-directional data exchange.
cidgoh/MISO_LIMS_Cloud
cidgoh/pathogen-mutation-functionalannotation-package
Package for functional annotation of mutations
cidgoh/snakemake_demo
cidgoh/training