What is Pheno-Ranker?
Pheno-Ranker is a command-line tool for individual-level comparison of phenotypic, clinical, and other categorical records. It was designed for GA4GH-oriented data such as Beacon v2 and Phenopackets v2, but it can also compare generic JSON, YAML, and CSV-derived datasets.
The primary interface is the pheno-ranker CLI. This makes it straightforward to use from a terminal, shell scripts, R/Python automation, workflow managers, and reproducible batch analyses. A Web App UI is also available for interactive use.
The central idea is simple: hierarchical records are flattened, transformed into one-hot encoded binary vectors, and compared with metrics such as Hamming distance and Jaccard similarity. This makes the same command-line workflow useful for cohort exploration, patient matching, clustering, multidimensional scaling, and graph analytics.
Pheno-Ranker is designed to be lightweight and fast for practical cohort analyses. The CLI workflow avoids database setup, uses compact binary representations internally, and can write sparse Matrix Market output for large all-vs-all comparisons when a dense matrix is unnecessary.
Key Features
- Native support for BFF and PXF inputs.
- Generic
JSON/YAMLsupport through configuration files. CSVsupport through the included csv2pheno-ranker utility.- Cohort mode for all-vs-all comparisons.
- Patient mode for ranking a target profile against a reference cohort.
- Include/exclude filters, variable weights, HPO ascendants, and exported intermediate files for inspection.
- Fast file-based execution with RAM-aware cohort comparison and optional sparse matrix output.
- Companion utilities for simulation, plotting, CSV import, and QR-code workflows.
Main Workflows
| Workflow | Purpose | Main output |
|---|---|---|
| Cohort mode | Compare all individuals or records in one or more cohorts. | matrix.txt |
| Patient mode | Rank reference records against a target patient or object. | rank.txt |
| Generic JSON | Compare non-GA4GH categorical records using a configuration file. | matrix.txt or rank.txt |
| Utilities | Prepare, simulate, plot, or encode data around the main ranking workflow. | Utility-specific files |
How to Use Pheno-Ranker
Pheno-Ranker is built on a robust Perl module, offering multiple interfaces for flexibility:
- Command-line Tool: For direct data processing and automation.
- Web App UI: A user-friendly interface for visual interaction.
Start with Download & Installation, then follow the Usage, Cohort mode, or Patient mode pages depending on your analysis.
Listen to the Paper: Audio Edition
Explore the key insights of Pheno-Ranker paper in audio format! Perfect for learning on the go or through immersive narration.
Made with Notebook LM