CNAG Biomedical Informatics

All

16 repositories

convert-pheno-ui
Public
The web UI for Convert-Pheno, a software toolkit for the interconversion of standard data models for phenotypic data
convert cdisc phenopackets omop-cdm beacon-friendly-format pheno-clinical
FreeMarker
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GNU General Public License v3.0
•1•4•2•60•Updated Oct 30, 2025Oct 30, 2025
omicsdm-documentation
Public
OmicsDM documentation
Makefile
•0•1•0•0•Updated Oct 27, 2025Oct 27, 2025
cbicall
Public
Shell
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GNU General Public License v3.0
•0•1•0•0•Updated Oct 24, 2025Oct 24, 2025
beacon2-cbi-tools
Public
Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)
json browser mongodb vcf microarray snp beacon data-exchange 23andme bff
Perl
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GNU General Public License v3.0
•9•3•0•0•Updated Oct 23, 2025Oct 23, 2025
OmicsDM
Public
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated Oct 15, 2025Oct 15, 2025
clarid-tools
Public
ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration
Perl
•0•2•0•0•Updated Oct 15, 2025Oct 15, 2025
convert-pheno
Public
A software toolkit for the interconversion of standard data models for phenotypic data
csv convert biomedical-informatics ehr beacon health-data cdisc redcap bff omop
Perl
•
Artistic License 2.0
•1•15•0•0•Updated Sep 26, 2025Sep 26, 2025
pheno-ranker
Public
Pheno-Ranker is a tool for comparing phenotypic data structured in JSON/YAML format, such as Beacon v2 Models or Phenopackets v2, as well as CSV.
yaml json bioinformatics csv genomics qrcode vcf biomedical-informatics semantic-similarity ehr
Perl
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Artistic License 2.0
•1•7•0•0•Updated Sep 4, 2025Sep 4, 2025
pheno-ranker-ui
Public
The web ui (R-Shiny application) for Pheno-Ranker, a tool designed for performing semantic similarity analysis on phenotypic data structured in JSON format, such as Beacon v2 Models or Phenopackets v2
json r shiny semantic-similarity data-exploration clinical-data semantic-similarity-measures beacon-v2 phenopackets-v2
R
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GNU General Public License v3.0
•0•2•0•35•Updated Jul 13, 2025Jul 13, 2025
sql.js-httpvfs-playground
Public
sql.js-httpvfs Playground
Svelte
•1•0•0•0•Updated Jul 3, 2025Jul 3, 2025
cbi-datahub
Public
MIT License
•0•0•0•0•Updated Jun 18, 2025Jun 18, 2025
omop-csv-validator
Public
The OMOP CSV Validator is a CLI tool that validates CSV files against JSON schemas generated from OMOP Common Data Model (CDM) DDL fiiles
linux schema csv perl postgresql ohdsi csv-validator json-validator omop-cdm cnag
Perl
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Artistic License 2.0
•0•2•0•0•Updated Apr 10, 2025Apr 10, 2025
omop-cdm-2-beacon-v2
Public
Jupyter Notebook
•0•0•0•0•Updated Dec 29, 2024Dec 29, 2024
.github
Public
Repository for modifying the organization's profile page
health-data
Makefile
•0•0•0•0•Updated Dec 8, 2024Dec 8, 2024
pheno-ranker-app
Public
A standalone desktop application for phenotype ranking using the Pheno-Ranker tool, built with Python and CustomTkinter.
Python
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MIT License
•0•1•0•0•Updated Nov 29, 2024Nov 29, 2024
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
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MIT License
•3.6k•0•0•0•Updated Sep 17, 2023Sep 17, 2023