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    109 repositories

    • cg

      Public
      Glue between Clinical Genomics apps
      Python
      •2•8•54•27•Updated Jan 3, 2025Jan 3, 2025

    • BALSAMIC

      Public
      Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
      bioinformaticsgenomicsvariant-callingsomatic-mutationssnakemake-workflows
      Python
      •
      MIT License
      •16•45•85•16•Updated Jan 3, 2025Jan 3, 2025

    • trailblazer

      Public
      Keep track of and manage analyses
      bioinformaticspython3
      Python
      •
      MIT License
      •2•6•7•2•Updated Jan 3, 2025Jan 3, 2025

    • scout

      Public
      VCF visualization interface
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •47•153•214•2•Updated Dec 20, 2024Dec 20, 2024

    • chanjo2

      Public
      Persistent coverage analysis tool using the d4 format
      Python
      •0•2•15•0•Updated Dec 20, 2024Dec 20, 2024

    • cg_lims

      Public
      Python
      •1•3•86•4•Updated Dec 19, 2024Dec 19, 2024

    • 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•2•15•1•Updated Dec 18, 2024Dec 18, 2024

    • schug

      Public
      All you need to know about genes, transcripts and exons
      Python
      •0•0•6•0•Updated Dec 17, 2024Dec 17, 2024

    • genmod

      Public
      Annotate models of genetic inheritance patterns in variant files (vcf files)
      Python
      •
      MIT License
      •19•78•22•3•Updated Dec 13, 2024Dec 13, 2024

    • genotype-api

      Public
      Rewrite of genotype package
      Python
      •1•0•13•1•Updated Dec 13, 2024Dec 13, 2024

    • chanjo-report

      Public
      Report generator for Chanjo output
      Python
      •
      MIT License
      •6•0•7•0•Updated Dec 10, 2024Dec 10, 2024

    • chanjo

      Public
      Chanjo provides a better way to analyze coverage data in clinical sequencing.
      pythoncoveragesqlgenomicsbiocondasambamba
      Python
      •
      MIT License
      •12•50•30•1•Updated Dec 10, 2024Dec 10, 2024

    • housekeeper

      Public
      File data orchestrator
      datafileorchestrator
      Python
      •
      MIT License
      •0•2•3•0•Updated Dec 9, 2024Dec 9, 2024

    • crunchy

      Public
      Compress fastq files with spring and check the integrity
      Python
      •
      MIT License
      •1•1•2•0•Updated Dec 9, 2024Dec 9, 2024

    • gens

      Public
      JavaScript
      •
      Mozilla Public License 2.0
      •5•1•7•2•Updated Dec 6, 2024Dec 6, 2024

    • docker-base-images

      Public
      A collection of useful images to be used as base images for Dockerfiles
      Dockerfile
      •
      MIT License
      •0•0•1•0•Updated Dec 4, 2024Dec 4, 2024

    • assets

      Public
      A repo which contains assets such as images
      0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • orderportal

      Public archive
      Clinical genomics web interface for placing orders
      1•1•8•0•Updated Dec 3, 2024Dec 3, 2024

    • 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/example/
      visualizationreportfusion-genes
      Python
      •
      GNU General Public License v3.0
      •10•26•2•0•Updated Nov 28, 2024Nov 28, 2024

    • .github

      Public
      Default community health files
      0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • hermes

      Public
      Communication layer between CG and the pipelines.
      Python
      •0•1•3•1•Updated Nov 26, 2024Nov 26, 2024

    • MUTANT

      Public
      Microbial Utility Toolbox And wrapper for data traNsmission and Transformation
      Python
      •
      GNU General Public License v3.0
      •1•0•28•3•Updated Nov 26, 2024Nov 26, 2024

    • 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•31•5•1•Updated Nov 25, 2024Nov 25, 2024

    • fluffy

      Public
      FetaL AneUploidy and FetalFraction analYsis Pipeline
      Python
      •8•3•0•0•Updated Nov 22, 2024Nov 22, 2024

    • preClinVar

      Public
      A ClinVar API submission helper written in FastAPI
      Python
      •
      MIT License
      •0•1•8•0•Updated Nov 21, 2024Nov 21, 2024

    • udni-tip2toe

      Public
      UDNI tip2toe deep phenotyping frontend
      Java
      •4•1•2•0•Updated Oct 31, 2024Oct 31, 2024

    • phenopacket-api

      Public
      Phenopacket API UDNI tip2toe backend for deep phenotyping
      TypeScript
      •
      MIT License
      •4•1•0•0•Updated Oct 31, 2024Oct 31, 2024

    • reference-files

      Public
      Small reference files
      Lua
      •2•5•2•1•Updated Oct 28, 2024Oct 28, 2024

    • raredisease

      Public
      CG's rare disease pipeline in next flow, see the main repo here 👇
      pipelineanalysisnextflowclinicalvariants
      Nextflow
      •
      MIT License
      •37•5•13•0•Updated Oct 10, 2024Oct 10, 2024

    • fusioncatcher

      Public
      Finder of Somatic Fusion Genes in RNA-seq data
      Python
      •
      GNU General Public License v3.0
      •68•0•0•0•Updated Oct 9, 2024Oct 9, 2024