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    135 repositories

    • guardians-doc

      Public
      Published documentation for UMCCR for the GUARDIANS project
      MDX
      •0•0•0•0•Updated Sep 7, 2026Sep 7, 2026

    • orcaglue

      Public
      OrcaGlue - Frontline ETL for Pipeline Automation Data Warehouse
      data-warehousewarehouse
      data-warehousewarehouse
      Python
      •0•0•0•1•Updated Sep 7, 2026Sep 7, 2026

    • wrapica

      Public
      A suite of secondary / tertiary functions for running ICA API calls
      Python
      •
      GNU General Public License v3.0
      •0•2•7•0•Updated Sep 4, 2026Sep 4, 2026

    • oncovault

      Public
      OncoVault - Comprehensive Data Warehouse for Pipeline Result
      data-warehousewarehouse
      data-warehousewarehouse
      Makefile
      •0•0•0•0•Updated Sep 3, 2026Sep 3, 2026

    • orcahouse

      Public
      🐳 UMCCR Pipeline & Workflow Data Warehouse
      data-warehousewarehouse
      data-warehousewarehouse
      HCL
      •0•0•0•0•Updated Sep 2, 2026Sep 2, 2026

    • orcavault

      Public
      OrcaVault - Comprehensive Data Warehouse for Pipeline Automation
      data-warehousewarehouse
      data-warehousewarehouse
      Shell
      •0•0•0•0•Updated Aug 27, 2026Aug 27, 2026

    • RNAsum

      Public
      Pipeline for generating RNAseq-based cancer patient reports
      rnaseq-pipelinernaseq-report
      rnaseq-pipelinernaseq-report
      R
      •
      Other
      •8•15•16•0•Updated Aug 24, 2026Aug 24, 2026

    • bolt

      Public
      UMCCR post-processing WGS logic and CLI tool
      Python
      •
      GNU General Public License v3.0
      •1•0•0•2•Updated Aug 20, 2026Aug 20, 2026

    • gpgr

      Public
      :books: Genomics Platform Group Reporter
      rcancer-genomics
      rcancer-genomics
      R
      •
      Other
      •2•10•4•3•Updated Aug 20, 2026Aug 20, 2026

    • terraform-provider-remscontent

      Public
      A Terraform provider to manage the *content* of a REMS instance
      Go
      •
      Mozilla Public License 2.0
      •0•0•4•3•Updated Aug 20, 2026Aug 20, 2026

    • steps-s3-copy

      Public
      A Steps orchestration for copying large volumes of S3 objects
      TypeScript
      •
      MIT License
      •0•1•14•0•Updated Aug 14, 2026Aug 14, 2026

    • curtrail

      Public
      A Python library that turns AWS and ICA bill/log data into neat and tidy Polars dataframes
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 14, 2026Aug 14, 2026

    • copyrite

      Public
      A CLI tool for efficient checksum/copy operations across object stores
      awsclouds3
      awsclouds3gcs
      Rust
      •
      MIT License
      •0•2•17•1•Updated Aug 13, 2026Aug 13, 2026

    • infrastructure

      Public
      Infrastructure as Code at UMCCR
      infrastructureawsterraform
      infrastructureawsterraform
      Python
      •8•11•16•3•Updated Aug 11, 2026Aug 11, 2026

    • sash

      Public
      UMCCR post-processing WGS workflow
      Nextflow
      •
      MIT License
      •0•2•3•4•Updated Aug 7, 2026Aug 7, 2026

    • nextflow-stack

      Public
      AWS stack to run Nextflow pipelines on Batch using shared resources
      Shell
      •1•0•5•3•Updated Aug 7, 2026Aug 7, 2026

    • htsget-deploy

      Public
      Deployment logic for htsget-rs
      TypeScript
      •
      MIT License
      •0•0•1•1•Updated Aug 4, 2026Aug 4, 2026

    • linxreport

      Public
      Linx Result Reporter
      R
      •
      Other
      •0•3•0•0•Updated Aug 4, 2026Aug 4, 2026

    • libica

      Public
      :snake: Python SDK for Illumina Connected Analytics (ICA) :dragon:
      Python
      •
      MIT License
      •4•5•0•1•Updated Aug 3, 2026Aug 3, 2026

    • htsget-rs

      Public
      A server implementation of the htsget protocol for bioinformatics in Rust
      rustbioinformaticsaws-lambda
      rustbioinformaticsaws-lambdaserverlesshtsgetbioinfonoodles
      Rust
      •
      MIT License
      •9•50•14•3•Updated Aug 3, 2026Aug 3, 2026

    • icav2-cli-plugins

      Public
      A set of additional subcommands for icav2
      Python
      •
      MIT License
      •0•3•38•1•Updated Jul 30, 2026Jul 30, 2026

    • gridss-purple-linx-nf

      Public
      Nextflow pipeline and AWS stack for the GRIDSS/PURPLE/LINX toolkit
      Python
      •1•4•0•1•Updated Jul 28, 2026Jul 28, 2026

    • k8tre

      Public
      Application for UMCCR deployment of k8tre
      Python
      •
      MIT License
      •13•0•0•1•Updated Jul 27, 2026Jul 27, 2026

    • k8tre-aws

      Public
      Infrastructure for UMCCR deployment of k8tre
      HCL
      •4•0•0•0•Updated Jul 27, 2026Jul 27, 2026

    • oncoglue

      Public
      OncoGlue - Frontline ETL for Pipeline Result Data Warehouse
      data-warehousewarehouse
      data-warehousewarehouse
      Jupyter Notebook
      •0•0•0•0•Updated Jul 17, 2026Jul 17, 2026

    • nf-ica

      Public
      Configurations and patches used to deploy nextflow pipelines onto ICAv2.
      0•0•0•1•Updated Jul 15, 2026Jul 15, 2026

    • nf-ica-cli

      Public
      CLI toolkit for orchestrating Nextflow pipeline deployments to Illumina Connected Analytics (ICA).
      GNU General Public License v3.0
      •0•0•0•1•Updated Jul 15, 2026Jul 15, 2026

    • sigrap

      Public
      :notes: Wrappers for somatic mutation signature analysis tools
      rcancer-genomics
      rcancer-genomics
      R
      •
      Other
      •0•5•2•0•Updated Jul 7, 2026Jul 7, 2026

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •4.1k•0•0•0•Updated Jul 3, 2026Jul 3, 2026

    • RNAsum.data

      Public
      RNAsum reference and test data
      Makefile
      •
      Other
      •0•0•1•0•Updated Jun 29, 2026Jun 29, 2026
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