This repository contains the analysis code and Jupyter notebooks associated with the manuscript “Cross-Cohort Prediction of Dental Caries and Periodontitis from Salivary Shotgun Metagenome Data.”
The repository includes workflows for:
- technical quality control and exploratory analysis;
- taxonomic and functional diversity analysis;
- differential abundance analysis;
- cross-validation, leave-one-study-out evaluation, and SHAP interpretation;
- generation of the main and supplementary figures.
Input data are not included in the repository. Data and output paths can be configured in config.py or through the SALIVARY_WGS_DATA_DIR and SALIVARY_WGS_OUTPUT_DIR environment variables.
Citation details will be added after publication.
MIT License.