A wrapper to the PheTK package.
Project description
PheQTK - The Phenotype Quick Toolkit
PheQTK is a Python package that wraps around PheTK.
Installation
In your All of Us jupyter notebook, install PheQTK using the following command:
!pip install --upgrade PheQTK
Usage
To start the PheQTK interface, run the following command:
from PheQTK import Quick
Quick.run()
You will be prompted to select a module. You can also select 'all' to run all modules.
If you run individual modules, you will be prompted to add required parameters for that module. Below is a list of the required parameters for each module:
- Cohort Module:
- a comma separated list of variant ids (20_13093478_G_A, 20_13093479_G_A, etc.)
-
Phecodes Module:
Roadmap
Currently, PheQTK only supports PheTK's Cohort Module. Additional modules will be added soon.
Contributing
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
License
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