All

16 repositories

convert-pheno
Public
A software toolkit for the interconversion of standard data models for phenotypic data
csv convert biomedical-informatics
csv convert biomedical-informatics ehr beacon health-data cdisc redcap bff omop
Perl
•
Artistic License 2.0
•1•15•1•0•Updated Apr 17, 2026Apr 17, 2026
clarid-tools
Public
ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration
Perl
•0•2•3•0•Updated Apr 1, 2026Apr 1, 2026
cbicall
Public
CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis…
python bash bioinformatics
python bash bioinformatics snakemake genomics json-schema ngs variant-calling ngs-analysis ngs-pipeline
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Mar 26, 2026Mar 26, 2026
beacon2-cbi-tools
Public
Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)
python json browser
python json browser mongodb perl vcf microarray snp beacon data-exchange
Perl
•
GNU General Public License v3.0
•0•3•0•0•Updated Mar 25, 2026Mar 25, 2026
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
yaml json bioinformatics csv genomics qrcode vcf biomedical-informatics semantic-similarity ehr
Perl
•
Artistic License 2.0
•1•7•0•1•Updated Mar 19, 2026Mar 19, 2026
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
convert cdisc phenopackets omop-cdm beacon-friendly-format pheno-clinical
FreeMarker
•
GNU General Public License v3.0
•1•5•2•67•Updated Feb 12, 2026Feb 12, 2026
OmicsDM
Public
HTML
•
GNU General Public License v3.0
•0•0•0•1•Updated Feb 6, 2026Feb 6, 2026
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, suc…
json r shiny
json r shiny semantic-similarity data-exploration clinical-data semantic-similarity-measures beacon-v2 phenopackets-v2
R
•
GNU General Public License v3.0
•0•2•0•38•Updated Jan 11, 2026Jan 11, 2026
omicsdm-documentation
Public
OmicsDM documentation
Makefile
•0•1•0•0•Updated Nov 28, 2025Nov 28, 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
linux schema csv perl postgresql ohdsi csv-validator json-validator omop-cdm cnag
Perl
•
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
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
•
MIT License
•0•1•0•0•Updated Nov 29, 2024Nov 29, 2024
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
•
MIT License
•3.9k•0•0•0•Updated Sep 17, 2023Sep 17, 2023

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CNAG Biomedical Informatics

All

All

16 repositories

convert-pheno

clarid-tools

cbicall

beacon2-cbi-tools

pheno-ranker

convert-pheno-ui

OmicsDM

pheno-ranker-ui

omicsdm-documentation

sql.js-httpvfs-playground

cbi-datahub

omop-csv-validator

omop-cdm-2-beacon-v2

.github

pheno-ranker-app

bioconda-recipes

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All

Repositories list

16 repositories