Pinned Repositories
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.
grdiamR
Functions to interact with the GRDI-AMR2 template.
mob-rgi-nf
A nextflow pipeline to detect AMR determinants and mobile genetic elements.
pathogen-genomics-package
This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
ReMarkable_templates
vmR
A set of R tools for interacting with the Virtual Microbial Database
genepio
The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.
rols
An R package to query EBI's Ontology Lookup Service (OLS)
wim-hof-breathing-helper
mob-suite
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
ejurga's Repositories
ejurga/ReMarkable_templates
ejurga/mob-rgi-nf
A nextflow pipeline to detect AMR determinants and mobile genetic elements.
ejurga/grdiamR
Functions to interact with the GRDI-AMR2 template.
ejurga/pathogen-genomics-package
This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
ejurga/vmR
A set of R tools for interacting with the Virtual Microbial Database