Documentation overview
Choose the comparison workflow that matches your data and question.
Pheno-Ranker compares structured phenotypic, clinical, and categorical
records in cohort mode or patient mode. This documentation covers input
preparation, command-line use, interpretation, and downstream analysis.
Find the Right Page
- Learn the concepts: What is Pheno-Ranker? and User Workflow.
- Install and run: Install & First Run, followed by the CLI reference.
- Choose a comparison: Cohort Mode for all-vs-all matrices or Patient Mode for target-to-reference ranking.
- Prepare input: Input Formats for BFF, PXF, CSV, and configured JSON/YAML.
- Continue downstream: Use Cases, Use from R, and companion utilities.
- Find technical or operational detail: Implementation, Algorithm, and FAQ.
Project Status
The documentation follows the current GitHub version of Pheno-Ranker; the latest CPAN release can differ between releases. Consult the Changes file for version-specific updates. The CLI is the primary interface, while the legacy Web App remains supported until 2027.
Project Links
GitHub repository · CPAN distribution · Publication and citation · Web App UI