genophenocorr 0.0.5

Search for genotype-phenotype correlations with GA4GH phenopackets

gpc

Genotype Phenotype Correlation

Set up

create a virtual envirnment. We will then need to install a specific version of setuptools

python3 -m venv venv
source venv/bin/activate
pip install "setuptools<58" --upgrade
pip install varcode

Then run this from the shell in which the venv has been activate (pysembl gets installed together with varcode) pyensembl install --release 107 --species homo_sapiens

Set up dependencies

pip install phenopackets
pip install pandas
pip install hpo-toolkit
pip install scipy
pip install statsmodels

Running notebooks

python3 -m venv venv
source venv/bin/activate
pip install .
pip install jupyter
python -m ipykernel install --name "venv" --display-name "venv"
cd notebooks
jupyter-notebook