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@CNAG-Biomedical-Informatics

CNAG Biomedical Informatics

README.md

Welcome to CNAG Biomedical Informatics!

We are a subdivision of the Biomedical Genomics Group at CNAG. Our research focuses on the development of tools for handling genomic and phenotypic data.

Mainly using Perl, Python, JavaScript (React) and R.

Tools

Convert-Pheno Convert-Pheno

A software toolkit for the interconversion of standard data models for phenotypic data

Published open access: Access the article by clicking here.
Playground Uptime Robot status
Documentation Perl Module Documentation Status
Documentation Web-UI Documentation Status
Code Repository Perl Module CPAN Publish
Code Repository Web-UI Docker build server & client

Pheno-Ranker

A toolkit for comparison of phenotypic data stored in GA4GH standards and beyond

Published open access: Access the article by clicking here
Playground Uptime Robot status
Documentation Perl Module Documentation Status
Documentation Web-UI Documentation Status
Code Repository Perl Module CPAN Publish
Code Repository Web-UI Docker build server & client

Pinned Loading

  1. convert-pheno-ui convert-pheno-ui Public

    The web UI for Convert-Pheno, a software toolkit for the interconversion of standard data models for phenotypic data

    FreeMarker 5 1

  2. pheno-ranker-ui 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

    R 2

  3. beacon2-cbi-tools beacon2-cbi-tools Public

    Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)

    Perl 3

  4. clarid-tools clarid-tools Public

    ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration

    Perl 2

  5. cbicall cbicall Public

    CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis-ready VCFs across heterogeneous comp…

    Python 1

Repositories

Showing 10 of 16 repositories
  • clarid-tools Public

    ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration

    CNAG-Biomedical-Informatics/clarid-tools’s past year of commit activity
    Perl 2 0 3 0 Updated Apr 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-ready VCFs across heterogeneous computing environments.

    CNAG-Biomedical-Informatics/cbicall’s past year of commit activity
    Python 1 GPL-3.0 0 0 0 Updated Mar 26, 2026
  • beacon2-cbi-tools Public

    Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)

    CNAG-Biomedical-Informatics/beacon2-cbi-tools’s past year of commit activity
    Perl 3 GPL-3.0 0 0 0 Updated Mar 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.

    CNAG-Biomedical-Informatics/pheno-ranker’s past year of commit activity
    Perl 7 Artistic-2.0 1 0 1 Updated Mar 19, 2026
  • convert-pheno Public

    A software toolkit for the interconversion of standard data models for phenotypic data

    CNAG-Biomedical-Informatics/convert-pheno’s past year of commit activity
    Perl 15 Artistic-2.0 1 0 0 Updated Mar 13, 2026
  • convert-pheno-ui Public

    The web UI for Convert-Pheno, a software toolkit for the interconversion of standard data models for phenotypic data

    CNAG-Biomedical-Informatics/convert-pheno-ui’s past year of commit activity
    FreeMarker 5 GPL-3.0 1 2 67 Updated Feb 12, 2026
  • OmicsDM Public
    CNAG-Biomedical-Informatics/OmicsDM’s past year of commit activity
    HTML 0 GPL-3.0 0 0 1 Updated Feb 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, such as Beacon v2 Models or Phenopackets v2

    CNAG-Biomedical-Informatics/pheno-ranker-ui’s past year of commit activity
    R 2 GPL-3.0 0 0 38 Updated Jan 11, 2026
  • omicsdm-documentation Public

    OmicsDM documentation

    CNAG-Biomedical-Informatics/omicsdm-documentation’s past year of commit activity
    Makefile 1 0 0 0 Updated Nov 28, 2025
  • sql.js-httpvfs-playground Public Forked from nishad/sql.js-httpvfs-playground

    sql.js-httpvfs Playground

    CNAG-Biomedical-Informatics/sql.js-httpvfs-playground’s past year of commit activity
    Svelte 0 1 0 0 Updated Jul 3, 2025
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