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    132 repositories

    • conda_recipes

      Public
      Conda recipes for GitHub tools not available from conda-forge/bioconda
      Shell
      •0•0•0•0•Updated Jun 4, 2026Jun 4, 2026

    • oncovault

      Public
      OncoVault - Comprehensive Data Warehouse for Pipeline Result
      Makefile
      •0•0•0•1•Updated Jun 4, 2026Jun 4, 2026

    • steps-s3-copy

      Public
      A Steps orchestration for copying large volumes of S3 objects
      TypeScript
      •
      MIT License
      •0•1•15•1•Updated Jun 3, 2026Jun 3, 2026

    • copyrite

      Public
      A CLI tool for efficient checksum/copy operations across object stores
      awsclouds3
      awsclouds3gcs
      Rust
      •
      MIT License
      •0•2•15•0•Updated Jun 3, 2026Jun 3, 2026

    • orcahouse

      Public
      🐳 UMCCR Pipeline & Workflow Data Warehouse
      HCL
      •0•0•0•1•Updated Jun 3, 2026Jun 3, 2026

    • sash

      Public
      UMCCR post-processing WGS workflow
      Nextflow
      •
      MIT License
      •0•1•7•1•Updated Jun 3, 2026Jun 3, 2026

    • bolt

      Public
      UMCCR post-processing WGS logic and CLI tool
      Python
      •
      GNU General Public License v3.0
      •1•0•4•2•Updated Jun 3, 2026Jun 3, 2026

    • RNAsum

      Public
      Pipeline for generating RNAseq-based cancer patient reports
      rnaseq-pipelinernaseq-report
      rnaseq-pipelinernaseq-report
      R
      •
      Other
      •7•12•17•1•Updated Jun 2, 2026Jun 2, 2026

    • rportal

      Public
      :crystal_ball: R functionality for UMCCR Data Portal
      R
      •
      Other
      •0•0•0•0•Updated Jun 2, 2026Jun 2, 2026

    • oncoglue

      Public
      OncoGlue - Frontline ETL for Pipeline Result Data Warehouse
      Shell
      •0•0•0•0•Updated Jun 2, 2026Jun 2, 2026

    • wrapica

      Public
      A suite of secondary / tertiary functions for running ICA API calls
      Python
      •
      GNU General Public License v3.0
      •0•2•8•1•Updated May 28, 2026May 28, 2026

    • orcavault

      Public
      OrcaVault - Comprehensive Data Warehouse for Pipeline Automation
      Shell
      •0•0•0•0•Updated May 28, 2026May 28, 2026

    • orcaglue

      Public
      Frontline ETL for Data Warehouse
      0•0•0•0•Updated May 27, 2026May 27, 2026

    • rems-deploy-ccgcm

      Public
      A Docker image of REMS built for deployment in AWS and setup for UMCCR configuration
      TypeScript
      •
      MIT License
      •0•0•0•4•Updated May 27, 2026May 27, 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•4•Updated May 27, 2026May 27, 2026

    • k8tre-aws

      Public
      Infrastructure for UMCCR deployment of k8tre
      HCL
      •3•0•0•0•Updated May 25, 2026May 25, 2026

    • k8tre

      Public
      Application for UMCCR deployment of k8tre
      Python
      •
      MIT License
      •11•0•0•0•Updated May 25, 2026May 25, 2026

    • gpgr

      Public
      :books: Genomics Platform Group Reporter
      rcancer-genomics
      rcancer-genomics
      R
      •
      Other
      •1•9•4•0•Updated May 24, 2026May 24, 2026

    • curation_docs

      Public
      Public documentation for curation team
      0•0•0•0•Updated May 22, 2026May 22, 2026

    • sigrap

      Public
      :notes: Wrappers for somatic mutation signature analysis tools
      rcancer-genomics
      rcancer-genomics
      R
      •
      Other
      •0•5•2•1•Updated May 22, 2026May 22, 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•6•Updated May 20, 2026May 20, 2026

    • libica

      Public
      :snake: Python SDK for Illumina Connected Analytics (ICA) :dragon:
      Python
      •
      MIT License
      •4•5•0•7•Updated May 16, 2026May 16, 2026

    • orcahouse-doc

      Public
      📘 Warehouse Documentation
      HTML
      •0•0•0•0•Updated May 14, 2026May 14, 2026

    • infrastructure

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

    • htsget-deploy

      Public
      Deployment logic for htsget-rs
      TypeScript
      •
      MIT License
      •0•0•0•1•Updated May 9, 2026May 9, 2026

    • aws-lambda-rust-runtime

      Public
      A Rust runtime for AWS Lambda
      Rust
      •
      Apache License 2.0
      •393•0•0•0•Updated May 8, 2026May 8, 2026

    • 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•13•12•3•Updated May 5, 2026May 5, 2026

    • terraform-common

      Public
      Common modules/units/stacks used by reference from our terraform infrastructure
      HCL
      •
      MIT License
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • curtrail

      Public
      A Python library that turns AWS and ICA bill/log data into neat and tidy Polars dataframes
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • oncoanalyser

      Public
      A comprehensive cancer DNA/RNA analysis and reporting pipeline
      Nextflow
      •
      MIT License
      •31•0•0•0•Updated Apr 21, 2026Apr 21, 2026
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