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FinnGen Handbook
  • Introduction
  • Where to begin
  • Background Concepts
  • FinnGen Data Specifics
  • Disease Specific Task Forces
  • Working in the Sandbox
    • How to get started with Sandbox
    • What is Sandbox and what can you do there
    • What do we mean by "red" and "green" data?
    • General workflows for the most common analyses
    • Quirks and Features
    • Which tools are available?
      • FinnGen exome query tool
      • Custom GWAS tools
      • Pipelines
      • Pre-installed Linux tools
      • PGS Browser
      • Lmod Linux tools
      • Anaconda Python module with ready set of scientific packages
      • Python packages
      • R packages
      • Atlas
      • BigQuery (relational database)
      • Atlas vs BigQuery cohorts
      • Genotype Browser
      • Jupyter
      • Cohort Operations tool (CO)
      • Trajectory Visualization Tool (TVT)
      • LifeTrack
      • Miscellaneous helper scripts/tools
        • Tool to annotate variants with RSIDs
        • Proper translations of medical, service sector and provider codes
        • BigQuery Connection – R
        • BigQuery Connection - Python
      • Sandbox internal API for software developers
    • Working with Phenotype Data
    • Working with Genotype Data
    • Running analyses in Sandbox
    • Billing information and where to find more details
  • Working outside the Sandbox
  • FAQ
  • Release Notes
  • Tool Catalog
  • Glossary
  • User Support
  • Data Protection & Security
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  1. Working in the Sandbox
  2. Which tools are available?

Miscellaneous helper scripts/tools

Tool to annotate variants with RSIDs

BigQuery Connection - Python

  • Downstream analysis - Active Ingredient - Bar plot

  • Case study - Sex difference - Pyramid plot

  • Case study - Comorbidity - Upset plot

  • Case study - Patient Timeline - Scatter plot

BigQuery Connection – R

  • Case study – All register data for a person

  • Case study – UpSet plot

  • Case study – Tornado plot

PreviousLifeTrackNextTool to annotate variants with RSIDs

Last updated 2 years ago

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