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    116 repositories

    • wrapica

      Public
      A suite of secondary / tertiary functions for running ICA API calls
      Python
      •
      GNU General Public License v3.0
      •0•2•14•0•Updated Aug 1, 2025Aug 1, 2025

    • htsget-rs

      Public
      A server implementation of the htsget protocol for bioinformatics in Rust
      rustbioinformaticsaws-lambdaserverlesshtsgetbioinfonoodles
      Rust
      •
      MIT License
      •10•45•14•2•Updated Aug 1, 2025Aug 1, 2025

    • htsget-deploy

      Public
      Deployment logic for htsget-rs
      TypeScript
      •
      MIT License
      •0•0•0•1•Updated Aug 1, 2025Aug 1, 2025

    • libica

      Public
      🐍 Python SDK for Illumina Connected Analytics (ICA) 🐉
      Python
      •
      MIT License
      •4•6•0•0•Updated Jul 31, 2025Jul 31, 2025

    • orca-ui

      Public
      TypeScript
      •
      MIT License
      •0•1•20•0•Updated Jul 31, 2025Jul 31, 2025

    • orcahouse

      Public
      🐳 UMCCR Pipeline & Workflow Data Warehouse
      HCL
      •0•0•12•0•Updated Jul 29, 2025Jul 29, 2025

    • docker-who

      Public
      A miscellaneous set of UMCCR dockerfiles that don't quite go anywhere else.
      Dockerfile
      •
      MIT License
      •0•3•1•0•Updated Jul 25, 2025Jul 25, 2025

    • bolt

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•2•1•Updated Jul 25, 2025Jul 25, 2025

    • orcabus

      Public
      We are moving to https://github.com/orcabus
      Python
      •0•5•28•0•Updated Jul 24, 2025Jul 24, 2025

    • infrastructure

      Public
      Infrastructure as Code at UMCCR
      awsterraforminfrastructure
      Python
      •8•10•11•4•Updated Jul 23, 2025Jul 23, 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•11•7•5•Updated Jul 22, 2025Jul 22, 2025

    • cwl-ica-cli

      Public
      The CLI used for creating/syncing CWL workflows from GitHub to ICAv1
      Python
      •
      MIT License
      •0•1•13•0•Updated Jul 22, 2025Jul 22, 2025

    • sash

      Public
      Nextflow
      •
      MIT License
      •0•0•2•1•Updated Jul 21, 2025Jul 21, 2025

    • pcgr

      Public
      Personal Cancer Genome Reporter (PCGR)
      R
      •
      MIT License
      •49•0•0•0•Updated Jul 17, 2025Jul 17, 2025

    • sigrap

      Public
      🎶 Wrappers for somatic mutation signature analysis tools
      rcancer-genomics
      R
      •
      Other
      •0•5•2•1•Updated Jul 16, 2025Jul 16, 2025

    • gpgr

      Public
      📚 Genomics Platform Group Reporter
      rcancer-genomics
      R
      •
      Other
      •1•9•2•1•Updated Jul 16, 2025Jul 16, 2025

    • cpsr

      Public
      Cancer Predisposition Sequencing Reporter (CPSR)
      R
      •
      Other
      •12•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • crypt4gh-rust

      Public
      Rust implementation for the Crypt4GH encryption format
      Rust
      •2•0•0•1•Updated Jul 11, 2025Jul 11, 2025

    • igv.js

      Public
      Embeddable genomic visualization component based on the Integrative Genomics Viewer
      HTML
      •
      MIT License
      •242•0•0•0•Updated Jul 3, 2025Jul 3, 2025

    • rportal

      Public
      🔮 R functionality for UMCCR Data Portal
      R
      •
      Other
      •0•0•1•0•Updated Jul 3, 2025Jul 3, 2025

    • gcs-deploy

      Public
      Python
      •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • datasets

      Public
      Metadata/github pages site for centre data
      MIT License
      •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • tgv

      Public
      Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion.
      Rust
      •
      MIT License
      •14•2•0•0•Updated Jul 1, 2025Jul 1, 2025

    • nextflow-stack

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

    • orcahouse-doc

      Public
      📘 Warehouse Documentation
      HTML
      •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • steps-s3-copy

      Public
      A Steps orchestration for copying large volumes of S3 objects
      TypeScript
      •
      MIT License
      •0•0•9•0•Updated Jun 30, 2025Jun 30, 2025

    • hmftools

      Public
      UMCCR custom fork of hmftools, mainly for Aarch64 migration testing purposes
      Java
      •
      GNU General Public License v3.0
      •61•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • agha-data-validation-pipeline

      Public
      Python
      •0•0•2•0•Updated Jun 24, 2025Jun 24, 2025

    • ega-submit

      Public
      EGA cryptor + Aspera CLI submitter
      Shell
      •0•0•0•0•Updated Jun 5, 2025Jun 5, 2025

    • bwa-mem2-perf

      Public
      CI benchmarking for bwa-mem2
      0•0•0•0•Updated Jun 2, 2025Jun 2, 2025