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.
pip install pheno_utils
Examples:
data = generate_synthetic_data(n=1000)
hist_ecdf_plots(data=data, col="val1")
age_refplots = GenderAgeRefPlot(data, "val1")
age_refplots.plot()
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.
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, 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, 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.
FAQs
Pheno data utils - viz, loaders, mergers
We found that pheno-utils demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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