pheno-utils

pheno-utils is a dynamic Python package developed by Pheno.AI, for handling our medical datasets. It simplifies data loading, enables effective merging, and offers intuitive visualization tools.

Install

pip install pheno_utils

How to use

Examples:

data = generate_synthetic_data(n=1000)
hist_ecdf_plots(data=data, col="val1")

age_refplots = GenderAgeRefPlot(data, "val1")
age_refplots.plot()

Setting Up pheno-utils

To use pheno-utils, you must have a config.json file. This file should be set up according to your filesystem and placed in the ~/.pheno/ directory.

If You’re Working on TRE

For those working in the Trusted Research Environment (TRE), you don’t need to worry about the config.json file. It will be automatically generated for you!

If You’re Working with Phenos’ S3 Bucket

If you’re working with Phenos’ S3 bucket, you’ll need to manually create the config.json file. You can do this by running the following Python script:

python config_setup/create_default_config.py -d s3://datasets_bucket_name

If you are working on local file system

If you are working on local file system, you’ll need to manually create the config.json file and locating it under ~/.pheno/ directory. Please use the config_setup/example_config.json as a template for your config.json file.