Phenofhy

API reference ​

Phenofhy is organized by workflow stage. Each module provides a small set of functions.

Modules ​

  • pipeline and load: metadata utilities and phenotype list helpers
  • extract: dataset extraction and SQL helpers
  • process: entity-specific processing and derivations
  • calculate: summary and prevalence statistics
  • profile: phenotype profile report
  • icd: ICD trait matching (pandas and Spark)
  • display: formatting helpers for categorical summaries
  • utils: DNAnexus helpers and file loading
  • _rules, _derive_funcs, _filter_funcs: lower-level building blocks