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@Clinical-Genomics Clinical Genomics

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    123 repositories

    • scout

      Public
      VCF visualization interface
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •51•180•245•6•Updated Aug 28, 2026Aug 28, 2026

    • oncorefiner

      Public
      Repo for secondary layer of WGS cancer analyses
      Nextflow
      •
      MIT License
      •1•1•7•9•Updated Aug 28, 2026Aug 28, 2026

    • cg

      Public
      Glue between Clinical Genomics apps
      Python
      •4•12•112•44•Updated Aug 28, 2026Aug 28, 2026

    • scout_loader

      Public
      A Rust-based loader that rapidly parses VCF files and creates new Scout cases with variants.
      Rust
      •
      MIT License
      •0•0•1•0•Updated Aug 28, 2026Aug 28, 2026

    • raredisease

      Public
      CG's rare disease pipeline in next flow, see the main repo here 👇
      pipelineanalysisnextflow
      pipelineanalysisnextflowclinicalvariants
      Nextflow
      •
      MIT License
      •70•6•14•1•Updated Aug 28, 2026Aug 28, 2026

    • oncoflow

      Public
      Pipeline cascade of nf-core/oncoanalyser + Clinical-Genomics/oncorefiner, written in Nextflow.
      Nextflow
      •
      MIT License
      •0•0•0•4•Updated Aug 28, 2026Aug 28, 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•18•1•Updated Aug 25, 2026Aug 25, 2026

    • reference-files

      Public
      Small reference files
      Lua
      •2•6•18•3•Updated Aug 24, 2026Aug 24, 2026

    • hermes

      Public
      Communication layer between CG and the pipelines.
      Python
      •0•1•3•4•Updated Aug 21, 2026Aug 21, 2026

    • housekeeper

      Public
      File data orchestrator
      datafileorchestrator
      datafileorchestrator
      Python
      •
      MIT License
      •0•2•1•1•Updated Aug 20, 2026Aug 20, 2026

    • genmod

      Public
      Annotate models of genetic inheritance patterns in variant files (vcf files)
      Python
      •
      MIT License
      •22•90•30•5•Updated Aug 18, 2026Aug 18, 2026

    • downsampling

      Public
      Downsample fastq files in an automated way
      Shell
      •4•12•3•0•Updated Aug 18, 2026Aug 18, 2026

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •527•0•0•1•Updated Aug 4, 2026Aug 4, 2026

    • BALSAMIC

      Public
      Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
      bioinformaticsgenomicsvariant-calling
      bioinformaticsgenomicsvariant-callingsomatic-mutationssnakemake-workflows
      Python
      •
      MIT License
      •15•59•85•12•Updated Jul 14, 2026Jul 14, 2026

    • trailblazer

      Public
      Keep track of and manage analyses
      bioinformaticspython3
      bioinformaticspython3
      Python
      •
      MIT License
      •2•6•6•4•Updated Jul 13, 2026Jul 13, 2026

    • oncoanalyser

      Public
      A comprehensive cancer DNA/RNA analysis and reporting pipeline
      Nextflow
      •
      MIT License
      •38•0•0•0•Updated Jul 9, 2026Jul 9, 2026

    • statina-ui

      Public
      Frontend app for Statina
      TypeScript
      •0•0•2•0•Updated Jul 6, 2026Jul 6, 2026

    • rdds

      Public
      Rare Disease Data Science & ML
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•121•4•Updated Jun 26, 2026Jun 26, 2026

    • fusion-report

      Public
      Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/exam…
      visualizationreportfusion-genes
      visualizationreportfusion-genes
      Python
      •
      GNU General Public License v3.0
      •13•28•6•1•Updated Jun 22, 2026Jun 22, 2026

    • fluffy

      Public
      FetaL AneUploidy and FetalFraction analYsis Pipeline
      Python
      •9•5•0•0•Updated Jun 11, 2026Jun 11, 2026

    • loqusdbapi

      Public
      A simple REST api for loqusdb
      Python
      •
      MIT License
      •0•1•10•0•Updated Jun 11, 2026Jun 11, 2026

    • patientMatcher

      Public
      A MatchMaker Exchange server
      genevariantsmatchmaker
      genevariantsmatchmakerscorematchmakingdiagnosissimilarity-scorehpo-similaritypatientsomim
      Python
      •
      MIT License
      •7•12•6•0•Updated Jun 1, 2026Jun 1, 2026

    • statina

      Public
      Python
      •3•2•20•0•Updated May 25, 2026May 25, 2026

    • gens

      Public
      TypeScript
      •
      Mozilla Public License 2.0
      •9•1•10•0•Updated May 20, 2026May 20, 2026

    • chanjo

      Public
      Chanjo provides a better way to analyze coverage data in clinical sequencing.
      pythoncoveragesql
      pythoncoveragesqlgenomicsbiocondasambamba
      Python
      •
      MIT License
      •12•50•32•2•Updated May 8, 2026May 8, 2026

    • chanjo-report

      Public
      Report generator for Chanjo output
      Python
      •
      MIT License
      •6•0•3•0•Updated May 8, 2026May 8, 2026

    • schug

      Public
      All you need to know about genes, transcripts and exons
      Python
      •
      MIT License
      •0•0•8•0•Updated May 8, 2026May 8, 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
      •8•42•6•0•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

    • metaflow

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