Welcome to pyPheWAS’s documentation!¶
The pyPheWAS module executes PheWAS analyses on large EMR datasets via command line tools. If this tools contributes to a scientific publication, please cite us:
Kerley, C.I., Chaganti, S., Nguyen, T.Q. et al. pyPheWAS: A Phenome-Disease Association Tool for Electronic Medical Record Analysis. Neuroinformatics (2022). https://doi.org/10.1007/s12021-021-09553-4
Kerley, C.I., Nguyen T.Q., Ramadass, K, et al. pyPheWAS Explorer: a visualization tool for exploratory analysis of phenome-disease associations. JAMIA Open (2023). https://doi.org/10.1093/jamiaopen/ooad018
Features¶
- Analysis of International Classification of Disease codes (both ICD-9 and ICD-10) and Current Procedural Terminology codes
- EMR data cleaning and preparation
- Compute mass logistic regressions on patient data
- Visualize results
- Examine relative novelty of disease-PheCode associations
- pyPheWAS Explorer: Interactive visualization of PheDAS experiments
- Sample synthetic EMR dataset
Latest Release: pyPheWAS 4.2.0¶
This release includes:
- Default regression equation modified to allow for both canonical and reversed PheWAS equations
- Updated plot styling to improve legibility
- Bug fix: can now run pyPhewasModel/pyProwasModel without covariates
- Other minor bug fixes
Support¶
If you are having issues, please let us know! Email me at:
License¶
This project is licensed under the MIT license.