DNAnexus learning resources

This page builds on the Environment and setup guide with external resources for learning the DNAnexus platform and TRE workflows.

Use it to strengthen prerequisite skills before running or extending Phenofhy analyses.

Prerequisites

Command-Line Fundamentals

• Bash for Bioinformatics - Intro to shell scripting for life scientists
• Best Practices on the DNAnexus Platform - Reproducible cloud research workflows

The DNAnexus Command-Line Interface (dx toolkit)

• Introduction to the CLI - Official DNAnexus Academy guide
• dx toolkit examples - Practical usage examples
• Getting started with dxdata - Intro notebook for the dxdata Python library

Our Future Health TRE Documentation

• TRE help documentation - Platform features and user guidance
• Our Future Health data documentation - Information on available datasets within the TRE
• Our Future Health researcher website - Researcher resources and application guidance

Phenotypic Data Analysis in JupyterLab

Loading and Exploring Data

• OFH-specific worked examples
• Loading cohorts and analysing phenotypic data - Cohort-to-analysis workflow
• Export participant data - Extract and save outputs
• Identifying participants with linked bulk files - Find participants with linked imaging or omics data

Genomic Data Analysis in JupyterLab

Getting Started with Hail

• Hail tutorial on DNAnexus - Intro to scalable genomic analysis on RAP
• GWAS tutorial (Hail documentation) - Step-by-step GWAS with Hail

Accessing and Linking Genomic Data

• UKB-RAP genomics notebooks - Worked examples for UK Biobank genetic data
• Linking genotypic and phenotypic data - Community guide for merging genetic and phenotypic datasets

Building Custom Applets and Pipelines

Documentation

• Building applets on DNAnexus - Official guide to packaging and deploying custom tools

Note: This resource list is maintained by Vincent Straub at the Leverhulme Centre for Demographic Science, University of Oxford. It is not affiliated with, endorsed by, or maintained by DNAnexus, UK Biobank, or Our Future Health.