phenoradar

Overview

PhenoRadar is a CLI tool for binary phenotype prediction from orthogroup-level TPM. Prepare input data in the separate phenoradar_prep repository, then supply the metadata and expression TSVs to PhenoRadar.

Install

pip install phenoradar

Fastest Run

Install the bundled compact test data, materialize default config, then run:

phenoradar dataset
phenoradar config
phenoradar run -c config.yml

Documentation (Recommended Order)

1. docs/quickstart.md: first successful run, full run, and prediction.
2. docs/data-format.md: required metadata/expression TSV schema.
3. docs/configuration.md: config behavior, defaults, and key-by-key definitions.
4. docs/cli-reference.md: all commands and options.
5. docs/output-artifacts.md: output files, column-level details, and interpretation guidance.
6. docs/pipeline-details.md: internal execution behavior.
7. docs/phylogenetic-imputation.md: optional phylogenetic context and disagreement candidates for unknown-species predictions.