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    124 repositories

    • htsget-rs

      Public
      A server implementation of the htsget protocol for bioinformatics in Rust
      rustbioinformaticsaws-lambdaserverlesshtsgetbioinfonoodles
      Rust
      •
      MIT License
      •10•46•14•4•Updated Oct 28, 2025Oct 28, 2025

    • copyrite

      Public
      A CLI tool for efficient checksum/copy operations across object stores
      awsclouds3gcs
      Rust
      •
      MIT License
      •0•2•16•2•Updated Oct 27, 2025Oct 27, 2025

    • sigrap

      Public
      🎶 Wrappers for somatic mutation signature analysis tools
      rcancer-genomics
      R
      •
      Other
      •0•5•2•1•Updated Oct 27, 2025Oct 27, 2025

    • rportal

      Public
      🔮 R functionality for UMCCR Data Portal
      R
      •
      Other
      •0•0•2•0•Updated Oct 27, 2025Oct 27, 2025

    • genocrate

      Public
      CLI suite for creating/validating genomics datasets
      HTML
      •
      Apache License 2.0
      •0•0•2•0•Updated Oct 27, 2025Oct 27, 2025

    • dracarys

      Public
      🐲 DRAGEN workflow tidying 🔥
      cancer-genomicsmultiqcr-packager6qcdragen
      R
      •
      Other
      •0•1•22•0•Updated Oct 26, 2025Oct 26, 2025

    • sash

      Public
      UMCCR post-processing WGS workflow
      Nextflow
      •
      MIT License
      •0•1•4•2•Updated Oct 24, 2025Oct 24, 2025

    • bolt

      Public
      UMCCR post-processing WGS logic and CLI tool
      Python
      •
      GNU General Public License v3.0
      •1•0•3•2•Updated Oct 24, 2025Oct 24, 2025

    • orcahouse

      Public
      🐳 UMCCR Pipeline & Workflow Data Warehouse
      HCL
      •0•0•13•0•Updated Oct 23, 2025Oct 23, 2025

    • curation_docs

      Public
      Public documentation for curation team
      0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • tidywigits

      Public
      🧬✨ Tidy Hartwig WiGiTS pipeline outputs
      cancer-genomicsr6
      R
      •
      Other
      •0•0•17•0•Updated Oct 21, 2025Oct 21, 2025

    • orcabus

      Public
      We are moving to https://github.com/orcabus
      Python
      •0•5•27•0•Updated Oct 20, 2025Oct 20, 2025

    • RNAsum

      Public
      Pipeline for generating RNAseq-based cancer patient reports
      rnaseq-pipelinernaseq-report
      R
      •
      Other
      •6•8•18•0•Updated Oct 17, 2025Oct 17, 2025

    • gpgr

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

    • WTS_workflow_results_comparison

      Public
      R
      •0•0•0•0•Updated Oct 15, 2025Oct 15, 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•12•9•3•Updated Oct 15, 2025Oct 15, 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 Oct 13, 2025Oct 13, 2025

    • homebrew-tap

      Public
      Homebrew Taps for UMCCR
      0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • homebrew-core

      Public
      🍻 Default formulae for the missing package manager for macOS (or Linux)
      Ruby
      •
      BSD 2-Clause "Simplified" License
      •13k•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • orca-ui

      Public
      TypeScript
      •
      MIT License
      •0•1•19•0•Updated Oct 13, 2025Oct 13, 2025

    • pcgr

      Public
      Personal Cancer Genome Reporter (PCGR)
      R
      •
      MIT License
      •48•0•0•0•Updated Oct 7, 2025Oct 7, 2025

    • wrapica

      Public
      A suite of secondary / tertiary functions for running ICA API calls
      Python
      •
      GNU General Public License v3.0
      •0•2•10•0•Updated Oct 5, 2025Oct 5, 2025

    • nemo

      Public
      🐠 Bioinfo Data Ocean Exploration
      rcancer-genomicsr6
      R
      •
      Other
      •0•0•4•0•Updated Oct 1, 2025Oct 1, 2025

    • oncoanalyser

      Public
      A comprehensive cancer DNA/RNA analysis and reporting pipeline
      Nextflow
      •
      MIT License
      •27•0•0•0•Updated Oct 1, 2025Oct 1, 2025

    • htsget-deploy

      Public
      Deployment logic for htsget-rs
      TypeScript
      •
      MIT License
      •0•0•0•1•Updated Sep 29, 2025Sep 29, 2025

    • oncokb-annotator

      Public
      Annotates variants in MAF with OncoKB annotation.
      Python
      •
      GNU Affero General Public License v3.0
      •64•0•0•0•Updated Sep 28, 2025Sep 28, 2025

    • gcs-deploy

      Public
      Python
      •0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • htsget-igv.js

      Public
      Locally develop with htsget-rs and IGV.js without CORS nuisances: NOT FOR PRODUCTION
      bioinformaticsgenomicshtsgetigvjs
      HTML
      •0•1•0•0•Updated Sep 25, 2025Sep 25, 2025

    • infrastructure

      Public
      Infrastructure as Code at UMCCR
      infrastructureawsterraform
      Python
      •8•11•13•3•Updated Sep 25, 2025Sep 25, 2025

    • libica

      Public
      🐍 Python SDK for Illumina Connected Analytics (ICA) 🐉
      Python
      •
      MIT License
      •4•6•0•0•Updated Sep 16, 2025Sep 16, 2025