Skip to content

@Clinical-Genomics Clinical Genomics

Change the repository type filter

All

    Repositories list

    116 repositories

    • cg

      Public
      Glue between Clinical Genomics apps
      Python
      •3•11•107•35•Updated Dec 27, 2025Dec 27, 2025

    • reference-files

      Public
      Small reference files
      Lua
      •2•5•8•2•Updated Dec 22, 2025Dec 22, 2025

    • BALSAMIC

      Public
      Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
      bioinformaticsgenomicsvariant-callingsomatic-mutationssnakemake-workflows
      Python
      •
      MIT License
      •15•57•84•12•Updated Dec 19, 2025Dec 19, 2025

    • scout

      Public
      VCF visualization interface
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •51•175•226•13•Updated Dec 19, 2025Dec 19, 2025

    • trailblazer

      Public
      Keep track of and manage analyses
      bioinformaticspython3
      Python
      •
      MIT License
      •2•6•5•3•Updated Dec 18, 2025Dec 18, 2025

    • hermes

      Public
      Communication layer between CG and the pipelines.
      Python
      •0•1•6•3•Updated Dec 17, 2025Dec 17, 2025

    • loqusdb

      Public
      A simple observation count database
      Python
      •
      MIT License
      •9•11•18•6•Updated Dec 16, 2025Dec 16, 2025

    • stranger

      Public
      Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
      bioinformaticslong-readlong-read-sequencingshort-tandem-repeatsmassively-parallel-sequencing
      Python
      •
      MIT License
      •6•37•10•0•Updated Dec 15, 2025Dec 15, 2025

    • genmod

      Public
      Annotate models of genetic inheritance patterns in variant files (vcf files)
      Python
      •
      MIT License
      •21•84•21•2•Updated Dec 15, 2025Dec 15, 2025

    • raredisease

      Public
      CG's rare disease pipeline in next flow, see the main repo here 👇
      pipelineanalysisnextflowclinicalvariants
      Nextflow
      •
      MIT License
      •55•6•14•1•Updated Dec 15, 2025Dec 15, 2025

    • chanjo2

      Public
      Persistent coverage analysis tool using the d4 format
      Python
      •
      MIT License
      •0•3•15•0•Updated Dec 9, 2025Dec 9, 2025

    • schug

      Public
      All you need to know about genes, transcripts and exons
      Python
      •
      MIT License
      •0•0•6•0•Updated Dec 4, 2025Dec 4, 2025

    • chanjo

      Public
      Chanjo provides a better way to analyze coverage data in clinical sequencing.
      pythoncoveragesqlgenomicsbiocondasambamba
      Python
      •
      MIT License
      •12•50•31•1•Updated Dec 3, 2025Dec 3, 2025

    • statina-ui

      Public
      Frontend app for Statina
      TypeScript
      •0•0•2•0•Updated Dec 2, 2025Dec 2, 2025

    • taxprofiler_metaval_cascade

      Public
      Chaining wrapper between taxprofiler and metaval
      0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • microSALT

      Public
      Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
      pipelinetypingclinicalresistancemicrobial
      Python
      •
      GNU General Public License v3.0
      •3•3•17•1•Updated Nov 25, 2025Nov 25, 2025

    • MIP

      Public
      Mutation Identification Pipeline. Read the latest documentation:
      pipelineanalysisclinicalvariants
      Perl
      •
      MIT License
      •10•47•10•1•Updated Nov 18, 2025Nov 18, 2025

    • chromograph

      Public
      Genetics graphing tool
      Python
      •
      MIT License
      •3•4•6•1•Updated Nov 14, 2025Nov 14, 2025

    • preClinVar

      Public
      A ClinVar API submission helper written in FastAPI
      Python
      •
      MIT License
      •0•1•7•0•Updated Nov 5, 2025Nov 5, 2025

    • rna-fx

      Public
      nf-core/rnafusion and gms/tomte chaining
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • chanjo-report

      Public
      Report generator for Chanjo output
      Python
      •
      MIT License
      •6•0•3•0•Updated Oct 29, 2025Oct 29, 2025

    • loqusdbapi

      Public
      A simple REST api for loqusdb
      Python
      •
      MIT License
      •0•1•9•0•Updated Oct 29, 2025Oct 29, 2025

    • udni-tip2toe

      Public
      UDNI tip2toe deep phenotyping frontend
      Java
      •4•1•5•0•Updated Oct 15, 2025Oct 15, 2025

    • MUTANT

      Public
      Microbial Utility Toolbox And wrapper for data traNsmission and Transformation
      Python
      •
      GNU General Public License v3.0
      •1•0•28•2•Updated Oct 14, 2025Oct 14, 2025

    • Scout-REViewer-service

      Public
      A rest service for generating REViewer output.
      Python
      •0•0•8•0•Updated Oct 3, 2025Oct 3, 2025

    • genotype-api

      Public
      Rewrite of genotype package
      Python
      •1•0•15•1•Updated Oct 2, 2025Oct 2, 2025

    • meatballs

      Public
      An open source recipe book from the awesome staff of Clinical Genomics
      Python
      •
      MIT License
      •1•2•4•29•Updated Sep 26, 2025Sep 26, 2025

    • housekeeper

      Public
      File data orchestrator
      datafileorchestrator
      Python
      •
      MIT License
      •0•2•3•0•Updated Sep 23, 2025Sep 23, 2025

    • phenopacket-api

      Public
      Phenopacket API UDNI tip2toe backend for deep phenotyping
      TypeScript
      •
      MIT License
      •4•1•0•0•Updated Sep 11, 2025Sep 11, 2025

    • gens

      Public
      JavaScript
      •
      Mozilla Public License 2.0
      •8•1•8•3•Updated Sep 8, 2025Sep 8, 2025