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    95 repositories

    • orcabus

      Public
       🐋 UMCCR Pipeline & Workflow Orchestration
      Python
      •0•5•58•7•Updated Feb 4, 2025Feb 4, 2025

    • orcahouse

      Public
      🐳 UMCCR Pipeline & Workflow Data Warehouse
      HCL
      •0•0•1•0•Updated Feb 4, 2025Feb 4, 2025

    • orca-ui

      Public
      TypeScript
      •
      MIT License
      •0•0•19•1•Updated Feb 4, 2025Feb 4, 2025

    • RNAsum

      Public
      Pipeline for generating RNAseq-based cancer patient reports
      rnaseq-pipelinernaseq-report
      R
      •
      Other
      •4•7•14•0•Updated Feb 4, 2025Feb 4, 2025

    • hts-specs

      Public
      Specifications of SAM/BAM and related high-throughput sequencing file formats
      TeX
      •176•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • infrastructure

      Public
      Infrastructure as Code at UMCCR
      awsterraforminfrastructure
      Python
      •8•10•13•3•Updated Feb 2, 2025Feb 2, 2025

    • nextflow-stack

      Public
      AWS stack to run Nextflow pipelines on Batch using shared resources
      Shell
      •0•0•2•3•Updated Feb 2, 2025Feb 2, 2025

    • rems-umccr

      Public
      A Docker image of REMS built for deployment in AWS and setup for UMCCR configuration
      TypeScript
      •
      MIT License
      •0•0•0•1•Updated Jan 30, 2025Jan 30, 2025

    • holmes

      Public
      BAM fingerprint stack
      TypeScript
      •
      MIT License
      •0•3•3•2•Updated Jan 29, 2025Jan 29, 2025

    • htsget-rs

      Public
      A server implementation of the htsget protocol for bioinformatics in Rust
      rustbioinformaticsaws-lambdaserverlesshtsgetbioinfonoodles
      Rust
      •
      MIT License
      •9•41•14•4•Updated Jan 24, 2025Jan 24, 2025

    • htsget-deploy

      Public
      Deployment logic for htsget-rs
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

    • crypt4gh-rust

      Public
      Rust implementation for the Crypt4GH encryption format
      Rust
      •2•0•0•1•Updated Jan 23, 2025Jan 23, 2025

    • data-portal-client

      Public
      UMCCR Data Portal Frontend
      TypeScript
      •1•1•6•4•Updated Jan 22, 2025Jan 22, 2025

    • dracarys

      Public
      🐲 DRAGEN workflow tidying 🔥
      cancer-genomicsmultiqcr-packager6qcdragen
      R
      •
      Other
      •0•0•26•0•Updated Jan 20, 2025Jan 20, 2025

    • MAF-summary

      Public
      Summary of a single or multiple MAF files.
      R
      •4•12•0•0•Updated Jan 20, 2025Jan 20, 2025

    • cwl-novice-tutorial

      Public
      CWL Novice Tutorial
      cwl
      HTML
      •
      Other
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • samplesheet-check-backend

      Public
      Python
      •0•0•2•1•Updated Jan 9, 2025Jan 9, 2025

    • samplesheet-check-frontend

      Public
      JavaScript
      •0•0•2•3•Updated Jan 9, 2025Jan 9, 2025

    • data-portal-apis

      Public
      UMCCR Data Portal API Backend in cloud native serverless
      Python
      •0•1•19•0•Updated Jan 2, 2025Jan 2, 2025

    • gene_panels

      Public
      R
      •0•0•1•0•Updated Dec 17, 2024Dec 17, 2024

    • sigrap

      Public
      🎶 Wrappers for somatic mutation signature analysis tools
      rcancer-genomics
      R
      •
      Other
      •0•5•2•0•Updated Dec 17, 2024Dec 17, 2024

    • gpgr

      Public
      📚 Genomics Platform Group Reporter
      rcancer-genomics
      R
      •
      Other
      •1•8•1•0•Updated Dec 17, 2024Dec 17, 2024

    • sk-explore

      Public
      HTML
      •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

    • conda_recipes

      Public
      Conda recipes for GitHub tools not available from conda-forge/bioconda
      Shell
      •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

    • woofr

      Public
      🐺 Helper code for woof
      r
      R
      •
      Other
      •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

    • cwl-ica

      Public
      A collection of cwl-ica workflows along with a user guide for the commands to use and contributions guide
      Common Workflow Language
      •
      MIT License
      •2•9•7•9•Updated Dec 10, 2024Dec 10, 2024

    • steps-s3-copy

      Public
      A Steps orchestration for copying large volumes of S3 objects
      TypeScript
      •
      MIT License
      •0•0•7•0•Updated Dec 9, 2024Dec 9, 2024

    • illumination

      Public
      🔆 Interacting with Illumina Connected Analytics (ICA) API
      expressejsnodejs
      EJS
      •2•3•1•1•Updated Dec 5, 2024Dec 5, 2024

    • libica

      Public
      🐍 Python SDK for Illumina Connected Analytics (ICA) 🐉
      Python
      •
      MIT License
      •4•6•4•1•Updated Dec 3, 2024Dec 3, 2024

    • rportal

      Public
      🔮 R functionality for UMCCR Data Portal
      R
      •
      Other
      •0•0•1•0•Updated Dec 2, 2024Dec 2, 2024