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@Clinical-Genomics Clinical Genomics

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    120 repositories

    • cg

      Public
      Glue between Clinical Genomics apps
      Python
      •3•11•106•38•Updated Apr 24, 2026Apr 24, 2026

    • scout

      Public
      VCF visualization interface
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •50•178•229•4•Updated Apr 24, 2026Apr 24, 2026

    • oncorefiner

      Public
      Repo for secondary layer of WGS cancer analyses
      Nextflow
      •
      MIT License
      •1•0•6•2•Updated Apr 24, 2026Apr 24, 2026

    • microSALT

      Public
      Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
      pipelinetypingclinical
      pipelinetypingclinicalresistancemicrobial
      Python
      •
      GNU General Public License v3.0
      •3•3•17•3•Updated Apr 24, 2026Apr 24, 2026

    • rdds

      Public
      Rare Disease Data Science & ML
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•111•3•Updated Apr 24, 2026Apr 24, 2026

    • stranger

      Public
      Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
      bioinformaticslong-readlong-read-sequencing
      bioinformaticslong-readlong-read-sequencingshort-tandem-repeatsmassively-parallel-sequencing
      Python
      •
      MIT License
      •7•41•6•0•Updated Apr 22, 2026Apr 22, 2026

    • statina-ui

      Public
      Frontend app for Statina
      TypeScript
      •0•0•3•3•Updated Apr 22, 2026Apr 22, 2026

    • bump2version-ci

      Public
      Repository to host automated bump2version CI to run on python repositories
      Shell
      •0•0•4•1•Updated Apr 18, 2026Apr 18, 2026

    • statina

      Public
      Python
      •3•2•18•0•Updated Apr 17, 2026Apr 17, 2026

    • hermes

      Public
      Communication layer between CG and the pipelines.
      Python
      •0•1•6•4•Updated Apr 15, 2026Apr 15, 2026

    • BALSAMIC

      Public
      Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
      bioinformaticsgenomicsvariant-calling
      bioinformaticsgenomicsvariant-callingsomatic-mutationssnakemake-workflows
      Python
      •
      MIT License
      •15•58•85•11•Updated Apr 13, 2026Apr 13, 2026

    • patientMatcher

      Public
      A MatchMaker Exchange server
      genevariantsmatchmaker
      genevariantsmatchmakerscorematchmakingdiagnosissimilarity-scorehpo-similaritypatientsomim
      Python
      •
      MIT License
      •7•12•6•0•Updated Apr 13, 2026Apr 13, 2026

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •497•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • trailblazer

      Public
      Keep track of and manage analyses
      bioinformaticspython3
      bioinformaticspython3
      Python
      •
      MIT License
      •2•6•7•4•Updated Apr 1, 2026Apr 1, 2026

    • fluffy

      Public
      FetaL AneUploidy and FetalFraction analYsis Pipeline
      Python
      •9•4•0•0•Updated Mar 30, 2026Mar 30, 2026

    • genmod

      Public
      Annotate models of genetic inheritance patterns in variant files (vcf files)
      Python
      •
      MIT License
      •21•89•25•4•Updated Mar 27, 2026Mar 27, 2026

    • taxprofiler_metaval_cascade

      Public
      Chaining wrapper between taxprofiler and metaval
      0•0•0•1•Updated Mar 27, 2026Mar 27, 2026

    • reference-files

      Public
      Small reference files
      Lua
      •2•6•10•1•Updated Mar 25, 2026Mar 25, 2026

    • housekeeper

      Public
      File data orchestrator
      datafileorchestrator
      datafileorchestrator
      Python
      •
      MIT License
      •0•2•3•0•Updated Mar 23, 2026Mar 23, 2026

    • meatballs

      Public
      An open source recipe book from the awesome staff of Clinical Genomics
      Python
      •
      MIT License
      •1•2•4•31•Updated Mar 11, 2026Mar 11, 2026

    • preClinVar

      Public
      A ClinVar API submission helper written in FastAPI
      Python
      •
      MIT License
      •0•1•9•0•Updated Mar 10, 2026Mar 10, 2026

    • nf-cascade

      Public
      A proof of concept daisy-chaining Nextflow workflows
      Nextflow
      •11•0•0•0•Updated Mar 10, 2026Mar 10, 2026

    • paraphrase

      Public
      Paraphase JSON parser
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 10, 2026Mar 10, 2026

    • gens

      Public
      JavaScript
      •
      Mozilla Public License 2.0
      •9•1•10•1•Updated Mar 3, 2026Mar 3, 2026

    • raredisease

      Public
      CG's rare disease pipeline in next flow, see the main repo here 👇
      pipelineanalysisnextflow
      pipelineanalysisnextflowclinicalvariants
      Nextflow
      •
      MIT License
      •63•6•16•1•Updated Mar 2, 2026Mar 2, 2026

    • mutacc-auto

      Public
      Scripts to run mutacc import functionality automatically
      Python
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • chanjo

      Public
      Chanjo provides a better way to analyze coverage data in clinical sequencing.
      pythoncoveragesql
      pythoncoveragesqlgenomicsbiocondasambamba
      Python
      •
      MIT License
      •12•50•31•2•Updated Feb 9, 2026Feb 9, 2026

    • loqusdb

      Public
      A simple observation count database
      Python
      •
      MIT License
      •9•11•20•7•Updated Jan 13, 2026Jan 13, 2026

    • genotype-api

      Public
      Rewrite of genotype package
      Python
      •1•0•15•1•Updated Dec 29, 2025Dec 29, 2025

    • chanjo2

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