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    71 repositories

    • talos

      Public
      Rare Disease variant reanalysis tool
      Python
      •
      MIT License
      •4•7•13•7•Updated Feb 8, 2025Feb 8, 2025

    • ClinvArbitration

      Public
      A side-project from the AIP, containing the code, logic, and documentation for the ClinVar consequence reassessment process in use at the CPG
      Python
      •
      MIT License
      •0•1•1•2•Updated Feb 8, 2025Feb 8, 2025

    • talos_manuscript

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•1•Updated Feb 7, 2025Feb 7, 2025

    • production-pipelines

      Public
      Genomics workflows for CPG using Hail Batch
      genome-analysishailseqrbioinformaticspipeline
      Python
      •
      MIT License
      •1•7•44•35•Updated Feb 7, 2025Feb 7, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•3•31•3•Updated Feb 6, 2025Feb 6, 2025

    • ourdna-browser

      Public
      HCL
      •
      MIT License
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • team-docs

      Public
      Documentation, guides, tips and tricks when working at the CPG
      Python
      •
      MIT License
      •1•1•3•8•Updated Feb 5, 2025Feb 5, 2025

    • metamist

      Public
      Sample level metadata system
      Python
      •
      MIT License
      •2•2•43•21•Updated Feb 5, 2025Feb 5, 2025

    • cpg-flow

      Public
      CPG Pipeline Python API
      Python
      •
      MIT License
      •0•0•3•2•Updated Feb 5, 2025Feb 5, 2025

    • images

      Public
      Reusable single-software docker images
      Dockerfile
      •
      MIT License
      •1•1•2•9•Updated Feb 5, 2025Feb 5, 2025

    • talos-azure-deploy

      Public
      Shell
      •
      MIT License
      •0•2•0•0•Updated Feb 4, 2025Feb 4, 2025

    • hail

      Public
      Scalable genomic data analysis.
      Python
      •
      MIT License
      •248•1•3•1•Updated Feb 2, 2025Feb 2, 2025

    • rare-disease

      Public
      A collection of scripts relating to rare-disease specific projects
      Python
      •
      MIT License
      •1•2•0•1•Updated Jan 31, 2025Jan 31, 2025

    • test_workflows_shared

      Public template
      Python
      •
      MIT License
      •0•0•0•1•Updated Jan 22, 2025Jan 22, 2025

    • cpg-infrastructure

      Public
      This repository is used to manage the infrastructure at the CPG
      Python
      •
      MIT License
      •1•3•6•4•Updated Jan 20, 2025Jan 20, 2025

    • sv-workflows

      Public
      Structural Variation Workflows
      Python
      •
      MIT License
      •2•1•2•10•Updated Jan 17, 2025Jan 17, 2025

    • variant-curation-portal

      Public
      Web application for curating loss of function variants
      Python
      •
      MIT License
      •1•1•5•0•Updated Jan 16, 2025Jan 16, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      TypeScript
      •
      MIT License
      •45•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • analysis-runner

      Public
      Python
      •
      MIT License
      •4•2•9•4•Updated Jan 16, 2025Jan 16, 2025

    • saige-tenk10k

      Public
      Hail batch pipeline to run SAIGE on CPG's GCP
      Python
      •
      MIT License
      •1•3•5•5•Updated Jan 16, 2025Jan 16, 2025

    • talos_af

      Public
      A Talos-like tool for identifying ACMG Actionable Findings in large cohorts
      MIT License
      •0•0•0•0•Updated Jan 5, 2025Jan 5, 2025

    • gnomad-deployments

      Public
      kustomizations for current gnomad project kubernetes deployments
      Makefile
      •1•0•0•0•Updated Jan 2, 2025Jan 2, 2025

    • cpg-utils

      Public
      Library of convenience functions specific to the CPG
      Python
      •
      MIT License
      •1•0•2•2•Updated Dec 17, 2024Dec 17, 2024

    • tgg-terraform-modules

      Public
      HCL
      •3•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • TRTools-segreg

      Public
      Toolkit for genome-wide analysis of tandem repeats
      Python
      •
      MIT License
      •22•0•0•0•Updated Nov 14, 2024Nov 14, 2024

    • TRTools-nonlinear-sum

      Public
      Toolkit for genome-wide analysis of tandem repeats
      Python
      •
      MIT License
      •22•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • gatk-sv

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •72•0•0•1•Updated Nov 13, 2024Nov 13, 2024

    • ourdna

      Public
      Python
      •
      MIT License
      •0•0•0•2•Updated Nov 11, 2024Nov 11, 2024

    • mocha-wgs

      Public
      A WDL workflow for running MoChA on WGS data
      WDL
      •2•0•0•0•Updated Nov 11, 2024Nov 11, 2024

    • cpg-python-template-repo

      Public template
      A template repository for python code, implementing the CPG setup guidelines
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024