.gitignore
.readthedocs.yml
LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
docs/Makefile
docs/alp_example/Feature_Importance.png
docs/alp_example/alkaline_phosphatase_genes_prs_exc_regressor_scatterplot.png
docs/alp_example/linear_assoc_alkaline_phosphatase_cov_200k_manhattan.png
docs/alp_example/linear_assoc_alkaline_phosphatase_cov_200k_qqplot.png
docs/association_results/linear_assoc_alanine_aminotransferase_cov_filtered.csv
docs/association_results/linear_assoc_alanine_aminotransferase_cov_filtered_manhattan.png
docs/association_results/linear_assoc_alanine_aminotransferase_cov_filtered_qqplot.png
docs/association_results/linear_assoc_albumin_cov_filtered.csv
docs/association_results/linear_assoc_albumin_cov_filtered_manhattan.png
docs/association_results/linear_assoc_albumin_cov_filtered_qqplot.png
docs/association_results/linear_assoc_alkaline_phosphatase_cov_filtered.csv
docs/association_results/linear_assoc_alkaline_phosphatase_cov_filtered_manhattan.png
docs/association_results/linear_assoc_alkaline_phosphatase_cov_filtered_qqplot.png
docs/association_results/linear_assoc_apolipoprotein_a_cov_filtered.csv
docs/association_results/linear_assoc_apolipoprotein_a_cov_filtered_manhattan.png
docs/association_results/linear_assoc_apolipoprotein_a_cov_filtered_qqplot.png
docs/association_results/linear_assoc_apolipoprotein_b_cov_filtered.csv
docs/association_results/linear_assoc_apolipoprotein_b_cov_filtered_manhattan.png
docs/association_results/linear_assoc_apolipoprotein_b_cov_filtered_qqplot.png
docs/association_results/linear_assoc_aspartate_aminotransferase_cov_filtered.csv
docs/association_results/linear_assoc_aspartate_aminotransferase_cov_filtered_manhattan.png
docs/association_results/linear_assoc_aspartate_aminotransferase_cov_filtered_qqplot.png
docs/association_results/linear_assoc_calcium_cov_filtered.csv
docs/association_results/linear_assoc_calcium_cov_filtered_manhattan.png
docs/association_results/linear_assoc_calcium_cov_filtered_qqplot.png
docs/association_results/linear_assoc_cholesterol_cov_filtered.csv
docs/association_results/linear_assoc_cholesterol_cov_filtered_manhattan.png
docs/association_results/linear_assoc_cholesterol_cov_filtered_qqplot.png
docs/association_results/linear_assoc_creactive_protein_cov_filtered.csv
docs/association_results/linear_assoc_creactive_protein_cov_filtered_manhattan.png
docs/association_results/linear_assoc_creactive_protein_cov_filtered_qqplot.png
docs/association_results/linear_assoc_creatinine_cov_filtered.csv
docs/association_results/linear_assoc_creatinine_cov_filtered_manhattan.png
docs/association_results/linear_assoc_creatinine_cov_filtered_qqplot.png
docs/association_results/linear_assoc_cystatin_c_cov_filtered.csv
docs/association_results/linear_assoc_cystatin_c_cov_filtered_manhattan.png
docs/association_results/linear_assoc_cystatin_c_cov_filtered_qqplot.png
docs/association_results/linear_assoc_direct_bilirubin_cov_filtered.csv
docs/association_results/linear_assoc_direct_bilirubin_cov_filtered_manhattan.png
docs/association_results/linear_assoc_direct_bilirubin_cov_filtered_qqplot.png
docs/association_results/linear_assoc_gamma_glutamyltransferase_cov_filtered.csv
docs/association_results/linear_assoc_gamma_glutamyltransferase_cov_filtered_manhattan.png
docs/association_results/linear_assoc_gamma_glutamyltransferase_cov_filtered_qqplot.png
docs/association_results/linear_assoc_glucose_cov_filtered.csv
docs/association_results/linear_assoc_glucose_cov_filtered_manhattan.png
docs/association_results/linear_assoc_glucose_cov_filtered_qqplot.png
docs/association_results/linear_assoc_glycated_haemoglobin_hba1c_cov_filtered.csv
docs/association_results/linear_assoc_glycated_haemoglobin_hba1c_cov_filtered_manhattan.png
docs/association_results/linear_assoc_glycated_haemoglobin_hba1c_cov_filtered_qqplot.png
docs/association_results/linear_assoc_hdl_cholesterol_cov_filtered.csv
docs/association_results/linear_assoc_hdl_cholesterol_cov_filtered_manhattan.png
docs/association_results/linear_assoc_hdl_cholesterol_cov_filtered_qqplot.png
docs/association_results/linear_assoc_igf1_cov_filtered.csv
docs/association_results/linear_assoc_igf1_cov_filtered_manhattan.png
docs/association_results/linear_assoc_igf1_cov_filtered_qqplot.png
docs/association_results/linear_assoc_ldl_direct_cov_filtered.csv
docs/association_results/linear_assoc_ldl_direct_cov_filtered_manhattan.png
docs/association_results/linear_assoc_ldl_direct_cov_filtered_qqplot.png
docs/association_results/linear_assoc_lipoprotein_a_cov_filtered.csv
docs/association_results/linear_assoc_lipoprotein_a_cov_filtered_manhattan.png
docs/association_results/linear_assoc_lipoprotein_a_cov_filtered_qqplot.png
docs/ldl_example/200k_maf001_ldl_adj_manhattan.png
docs/ldl_example/200k_maf001_ldl_adj_qqplot.png
docs/ldl_example/Feature_Importance.png
docs/ldl_example/Prediction_Error.png
docs/ldl_example/Residuals.png
docs/ldl_example/regressor_scatterplot.png
docs/source/1920px-Beta_distribution_pdf.svg.png
docs/source/cli.rst
docs/source/computation.rst
docs/source/conf.py
docs/source/index.rst
docs/source/methods_comparison.rst
docs/source/model_types.rst
docs/source/neg_log.png
docs/source/pipeline.rst
docs/source/real_cases.rst
docs/source/use_example.rst
docs/source/utils.rst
docs/source/biomarkers/alanine_aminotransferase.rst
docs/source/biomarkers/albumin.rst
docs/source/biomarkers/alkaline_phosphatase.rst
docs/source/biomarkers/apolipoprotein_a.rst
docs/source/biomarkers/apolipoprotein_b.rst
docs/source/biomarkers/aspartate_aminotransferase.rst
docs/source/biomarkers/cholesterol.rst
docs/source/biomarkers/creactive_protein.rst
docs/source/biomarkers/creatinine_serum.rst
docs/source/biomarkers/hdl.rst
docs/source/biomarkers/ldl.rst
scripts/betareg_shell.R
scripts/plot_script.R
src/GenRisk.egg-info/PKG-INFO
src/GenRisk.egg-info/SOURCES.txt
src/GenRisk.egg-info/dependency_links.txt
src/GenRisk.egg-info/entry_points.txt
src/GenRisk.egg-info/not-zip-safe
src/GenRisk.egg-info/requires.txt
src/GenRisk.egg-info/top_level.txt
src/genrisk/__init__.py
src/genrisk/__main__.py
src/genrisk/association_analysis.py
src/genrisk/cli.py
src/genrisk/gene_scoring.py
src/genrisk/helpers.py
src/genrisk/pipeline.py
src/genrisk/prediction_models.py
src/genrisk/prs_scoring.py
src/genrisk/utils.py
toy_example/README.md
toy_example/betareg_assoc_quan.tsv
toy_example/betareg_assoc_quan_manhattan.png
toy_example/betareg_assoc_quan_qqplot.png
toy_example/genes_info_ref.txt
toy_example/info.pheno
toy_example/linear_assoc_quan.tsv
toy_example/linear_assoc_quan_manhattan.png
toy_example/linear_assoc_quan_qqplot.png
toy_example/load_models.ipynb
toy_example/logit_assoc_binary.tsv
toy_example/logit_assoc_binary_manhattan.png
toy_example/logit_assoc_binary_qqplot.png
toy_example/toy_dataset_feats.tsv
toy_example/toy_genes_scores.tsv
toy_example/binary_classifier_model/Precision Recall.png
toy_example/binary_classifier_model/Precision_Recall.png
toy_example/binary_classifier_model/binary_classifier_model.pkl
toy_example/binary_classifier_model/binary_classifier_model_classifier_confusion_matrix.png
toy_example/binary_classifier_model/binary_classifier_model_compare_models.tsv
toy_example/binary_classifier_model/binary_classifier_model_external_testing_results.tsv
toy_example/binary_classifier_model/binary_classifier_model_report.txt
toy_example/binary_classifier_model/binary_classifier_model_tuned_model.tsv
toy_example/binary_classifier_model/feature.png
toy_example/quan_regression_model/Prediction Error.png
toy_example/quan_regression_model/Prediction_Error.png
toy_example/quan_regression_model/Residuals.png
toy_example/quan_regression_model/feature.png
toy_example/quan_regression_model/quan_regression_model.pkl
toy_example/quan_regression_model/quan_regression_model_compare_models.tsv
toy_example/quan_regression_model/quan_regression_model_external_testing_results.tsv
toy_example/quan_regression_model/quan_regression_model_regressor_scatterplot.png
toy_example/quan_regression_model/quan_regression_model_report.txt
toy_example/quan_regression_model/quan_regression_model_tuned_model.tsv