User Workflow
The typical Pheno-Ranker workflow has four stages: prepare input data, run a comparison, inspect or visualize the outputs, and optionally use companion utilities. Start with your data format, choose the comparison mode, then follow the output to the analysis or utility page that matches your task.
These stages apply to both Desktop and the CLI. Desktop provides input selection and result viewers; the CLI exposes the same analysis engine for terminal and scripted workflows.
Prepare data
Start from BFF or PXF, convert another clinical standard to BFF, configure generic JSON/YAML, or prepare arbitrary tabular data with csv2pheno-ranker.
Compare records
Select cohort mode for all-vs-all comparisons or patient mode to rank matches against a target patient. In Desktop, choose the mode in Setup; from the CLI, supplying a target selects patient mode.
Analyze outputs
Explore rankings, pair comparisons, and cohort plots in Desktop, or open the saved outputs in R and other analysis tools.
Use utilities
Use the Desktop Tools menu or the companion CLI utilities to simulate data, import CSV files, plot BFF/PXF summaries, or encode vectors as QR codes.
Companion Utilities
