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@va-big-data-genomics VA Big Data Genomics Group

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    13 repositories

    • va-big-data-genomics.github.io

      Public
      GitHub Pages site for VA Big Data Genomics group
      HTML
      •2•1•2•0•Updated Jan 16, 2025Jan 16, 2025

    • trellis-mvp-functions

      Public
      Trellis serverless data management framework for variant calling of VA MVP whole-genome sequencing data.
      Python
      •1•6•15•2•Updated Jun 18, 2024Jun 18, 2024

    • data-release-portal

      Public
      Source for web portal describing data releases published by the Stanford Data-as-a-Service (DaaS) team.
      MIT License
      •0•0•2•0•Updated Aug 30, 2023Aug 30, 2023

    • trellisdata

      Public
      Python package with classes and methods used in implementing a Trellis data management system.
      Python
      •
      MIT License
      •1•0•7•0•Updated Jul 5, 2023Jul 5, 2023

    • trellis-mvp-data-modelling

      Public
      Resources uses for interacting and updating the Trellis MVP graph database model.
      Python
      •
      MIT License
      •0•0•3•0•Updated May 12, 2023May 12, 2023

    • dockerfiles

      Public
      Dockerfiles for creating Docker images
      Roff
      •
      MIT License
      •0•0•0•0•Updated May 8, 2023May 8, 2023

    • general-practices

      Public
      Documentation of effective practices used in the Stanford Center for Genomics& Personalized Medicine.
      MIT License
      •1•2•2•0•Updated Mar 14, 2023Mar 14, 2023

    • .github

      Public
      1•0•0•0•Updated Jan 13, 2023Jan 13, 2023

    • trellis-mvp-gatk

      Public
      GATK with five-dollar-genome-analysis-pipeline on GCP for MVP
      WDL
      •0•2•1•0•Updated Nov 1, 2022Nov 1, 2022

    • trellis-mvp-sv-callers

      Public
      Repository of structural variant calling resources used by Trellis to analyze whole-genome sequencing data generated as part of the Department of Veterans Affairs Million Veteran Program (MVP)
      Shell
      •0•0•1•1•Updated Oct 21, 2022Oct 21, 2022

    • variant-analysis-on-bigquery

      Public
      Analyzing genomic data uploaded to BigQuery using the Variant Transforms tool
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jun 23, 2022Jun 23, 2022

    • trellis-mvp-terraform

      Public
      Trellis MVP Terraform configurations
      HCL
      •
      MIT License
      •1•1•2•0•Updated Jun 8, 2021Jun 8, 2021

    • trellis-mvp-analysis

      Public
      Jupyter notebooks for analyzing $5 GATK (GATK-MVP) invoked in the Trellis Data management system using Neo4J graph DB and Google Cloud
      Jupyter Notebook
      •0•2•0•0•Updated Jan 29, 2021Jan 29, 2021