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    106 repositories

    • gatk-bwamem-jni

      Public
      JNI code for bwa mem
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 8, 2025Mar 8, 2025

    • orcabus

      Public
       🐋 UMCCR Pipeline & Workflow Orchestration
      Python
      •0•5•70•10•Updated Mar 7, 2025Mar 7, 2025

    • oncoanalyser-aws-example-setup

      Public
      An example of setting up Oncoanalyser in AWS
      TypeScript
      •
      MIT License
      •0•0•0•1•Updated Mar 7, 2025Mar 7, 2025

    • orca-ui

      Public
      TypeScript
      •
      MIT License
      •0•1•17•2•Updated Mar 7, 2025Mar 7, 2025

    • orcahouse-doc

      Public
      📘 Warehouse Documentation
      HTML
      •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • orcahouse

      Public
      🐳 UMCCR Pipeline & Workflow Data Warehouse
      HCL
      •0•0•1•0•Updated Mar 6, 2025Mar 6, 2025

    • dracarys

      Public
      🐲 DRAGEN workflow tidying 🔥
      cancer-genomicsmultiqcr-packager6qcdragen
      R
      •
      Other
      •0•0•30•0•Updated Mar 6, 2025Mar 6, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.4k•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • 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•4•Updated Mar 6, 2025Mar 6, 2025

    • hmftools

      Public
      Various algorithms for analysing genomics data
      Java
      •
      GNU General Public License v3.0
      •60•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • oncoanalyser-aws

      Public
      TypeScript
      •1•0•6•0•Updated Mar 5, 2025Mar 5, 2025

    • oncoanalyser-arm64

      Public
      ARM64 experiments for Oncoanalyser
      Nextflow
      •
      MIT License
      •15•0•0•0•Updated Mar 5, 2025Mar 5, 2025

    • pcgr

      Public
      Personal Cancer Genome Reporter (PCGR)
      R
      •
      MIT License
      •48•0•0•0•Updated Mar 5, 2025Mar 5, 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•0•Updated Mar 5, 2025Mar 5, 2025

    • sk-explore

      Public
      HTML
      •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

    • sash

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • bolt

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•2•1•Updated Mar 2, 2025Mar 2, 2025

    • bwa

      Public
      Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
      C
      •
      Apache License 2.0
      •556•0•0•0•Updated Feb 28, 2025Feb 28, 2025

    • nextflow-stack

      Public
      AWS stack to run Nextflow pipelines on Batch using shared resources
      Shell
      •1•0•2•3•Updated Feb 27, 2025Feb 27, 2025

    • pmcc-aws

      Public
      PMCC AWS Setup
      MIT License
      •0•0•0•0•Updated Feb 24, 2025Feb 24, 2025

    • crypt4gh-rust

      Public
      Rust implementation for the Crypt4GH encryption format
      Rust
      •2•0•0•1•Updated Feb 24, 2025Feb 24, 2025

    • cpsr

      Public
      Cancer Predisposition Sequencing Reporter (CPSR)
      R
      •
      Other
      •12•0•0•0•Updated Feb 24, 2025Feb 24, 2025

    • infrastructure

      Public
      Infrastructure as Code at UMCCR
      awsterraforminfrastructure
      Python
      •8•10•14•3•Updated Feb 21, 2025Feb 21, 2025

    • gpgr

      Public
      📚 Genomics Platform Group Reporter
      rcancer-genomics
      R
      •
      Other
      •1•8•1•0•Updated Feb 21, 2025Feb 21, 2025

    • htsget-deploy

      Public
      Deployment logic for htsget-rs
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Feb 19, 2025Feb 19, 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 Feb 18, 2025Feb 18, 2025

    • holmes

      Public
      BAM fingerprint stack
      TypeScript
      •
      MIT License
      •0•3•3•3•Updated Feb 12, 2025Feb 12, 2025

    • hts-specs

      Public
      Specifications of SAM/BAM and related high-throughput sequencing file formats
      TeX
      •176•0•0•0•Updated Feb 12, 2025Feb 12, 2025

    • rportal

      Public
      🔮 R functionality for UMCCR Data Portal
      R
      •
      Other
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • MAF-summary

      Public
      Summary of a single or multiple MAF files.
      R
      •4•12•0•0•Updated Feb 5, 2025Feb 5, 2025