ukbeaver 0.3.0

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ukbeaver 🦫

A lightweight toolkit for working with UK Biobank (UKB) tabular and imaging data

UK Biobank (UKB) provides one of the world’s largest biomedical datasets, containing extensive tabular information (phenotypes, biomarkers, questionnaires, etc.) and imaging data (MRI, retinal scans, X-rays, etc.). While rich in potential, accessing and organizing UKB data can be cumbersome due to its complex file structures, field IDs, and modality-specific formats.

ukbeaver is designed to streamline this process. It provides a convenient interface to:

• 🗂 Access and organize tabular data — handle field IDs, instances, and arrays with ease.
• 🖼 Work with imaging data — load and manage different modalities without manual overhead.
• 🔎 Query efficiently — simplify the process of extracting subsets of data for analysis.
• ⚡ Integrate with existing workflows — built to be lightweight, flexible, and compatible with Python data science tools.

With ukbeaver, researchers can focus on analysis and discovery, instead of wrestling with data preprocessing.

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🚀 Getting Started

Installation

pip install ukbeaver

Minimal Example

from ukbeaver.tabular import Phenotype

# init with a UKB-style tab-delimited file
ph = Phenotype("pheno_table.tsv")

# load everything
df, field_map = ph.get_df()

# select specific field IDs
df_50, _ = ph.get_df(fids=["50"])

# select only instance 0
df_i0, _ = ph.get_df(ins=0)

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⚠️ Note: Access to UK Biobank data requires an approved UKB project application. ukbeaver does not bypass these restrictions; it only assists in handling datasets you are authorized to use.