usher-exploring

Go to file

gbanyan 0e89bf0dd6 docs(03-02): complete expression evidence layer plan

- Create 03-02-SUMMARY.md with performance metrics, decisions, and deviations
- Update STATE.md: 5 of 6 plans complete in Phase 03 (03-06 remaining)
- Update progress: 55% complete (11/20 plans across all phases)
- Add key decisions: Tau calculation, expression scoring, CellxGene optional
- Record duration: 12 min for 2 tasks (9 files modified)
- Self-check passed: all files and commits verified

Expression layer provides:
- HPA/GTEx tissue expression with Tau specificity index
- Usher-tissue enrichment scoring (retina, inner ear, cilia)
- Optional CellxGene single-cell integration
- CLI command with checkpoint-restart
- 11 passing unit and integration tests

2026-02-11 19:12:18 +08:00

.planning

docs(03-02): complete expression evidence layer plan

2026-02-11 19:12:18 +08:00

config

feat(01-01): create Python package scaffold with config system

2026-02-11 16:24:35 +08:00

src/usher_pipeline

docs(03-04): complete subcellular localization evidence layer

2026-02-11 19:08:01 +08:00

tests

docs(03-04): complete subcellular localization evidence layer