biobanking 0.0.8

Biobanking data processing, annotation, and association workflows

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

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/*