pgscatalog.calc

This Python package contains:

• CLI applications to aggregate and adjust calculated polygenic scores (PGS) in the context of genetic ancestry similarity
• library classes and functions for working with calculated PGS and PCA data

[!NOTE]

• This package doesn't contain functionality to calculate a PGS from target genomes and scoring files
• If you want software that does that, check out the PGS Catalog Calculator
• This package is focused on PGS aggregation and normalisation, and is used internally by the PGS Catalog Calculator

If you want to write Python code to work with PGS data, the library may be helpful for you.

Installation

or install via pip:

$ pipx install pgscatalog.calc

Documentation

Documentation is available at https://pygscatalog.readthedocs.io/.

Developer instructions

You'll need nox and uv installed.

To get set up with a development environment run:

$ nox -s dev
$ source .venv/bin/activate

This will create a virtual environment in the current directory.

$ pgscatalog-aggregate --help

nox can also be used to run tests and lint the package:

$ nox