Metadata-Version: 2.4
Name: biobanking
Version: 0.0.8
Summary: Biobanking data processing, annotation, and association workflows
Author: Deepro Banerjee
License: MIT License
        
        Copyright (c) 2026 Deepro Banerjee
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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Keywords: genomics,biobanks,rvas,phewas
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: scikit-learn
Requires-Dist: tqdm
Requires-Dist: pyarrow
Requires-Dist: gcsfs
Requires-Dist: google-cloud-storage
Requires-Dist: pandas-gbq
Requires-Dist: phetk
Dynamic: license-file

# Biobanking
Systematic collection, processing, storage, and analysis of biological samples and associated health records for medical research.

# Supported pipelines
## Preprocess
Contains biobank specific modules with scripts for EHR data collection, cleaning and processing.

## QC (Under construction) 
Will contain biobank specific modules with scripts for variant quality control and filtering.

## Annotation (Under construction)
Will contain biobank specific modules with scripts for variant annotation.

## Association
Contains biobank specific modules with scripts for genotype-phenotype association tests.

# Supported biobanks
## All of Us
The All of Us biobank consists of coupled whole genome sequencing and electronic health record data of 430k individuals with a plan to extend up to a million.

## UK Biobank (Under construction)
The UK Biobank consists of coupled whole genome sequencing and electronic health record data of ~500k participants.

# Internal Use
```bash
python -m pip install -U pip build
pip install twine
# linux
rm -rf dist build *.egg-info src/*.egg-info
# windows
Remove-Item -Recurse -Force dist, *.egg-info, src\*.egg-info
python -m build
pip install dist/biobanking-0.0.8-py3-none-any.whl
python -c "from biobanking.association.aou import REGENIE; regenie = REGENIE(); from biobanking.preprocess.aou.measurements import save_measurements_in_wide_format; print('import ok')"
twine upload dist/*
```
