Our Future Health Example TRE Notebooks

This public repository contains example code scripts in the form of interactive Python notebooks (.ipynb) to help Our Future Health Trusted Research Environment (TRE) users get started with the resource.

Folders

• Python Notebooks
  • OFHP1_Phenotype_Prep_for_GWAS_Python.ipynb - Example script for Python users preparing phenotypic data for a case/control GWAS within the TRE resource
• R Notebooks
  • OFHR1_Data_Extraction_R.ipynb - Example script for R users on extracting Our Future Health data for use in downstream analyses within the TRE resource
  • OFHR2_Epidemiological_Analysis_Workflow_R.ipynb - Example script for an end-to-end analytical workflow within the Our Future Health TRE using R
• Bash Notebooks
  • OFHB1_Phenotype_Prep_for_GWAS_Bash.ipynb - Example script for Bash users preparing phenotypic data for a case/control GWAS within the TRE resource, and a generalizable approach to using swiss-army-knife for bioinformatics tasks

Each script contains example code, as well as accompanying information in the form of markdown text and comments. All files can be freely downloaded for usage within the Our Future Health TRE.

Wider information

For more information on how to work within the Our Future Health TRE please refer to:

• Our Future Health TRE help documentation for information on features and functionality within the TRE
• Our Future Health data documentation for information on the data that is available within the TRE
• Our Future Health researcher website for general information about researcher resources within Our Future Health and how to apply

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For questions or queries, please contact access@ourfuturehealth.org.uk