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c7b6649d31
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Week 1: Tier-A sickle cell signature via 2-study concordance
Implement and run the Week 1 disease-signature pipeline:
- src/disease.py: Welch t-test + BH DE (microarray), probe->symbol
collapse, cross-study concordance filter, 2-study provenance schema
- scripts/week1_explore.py: download GSE35007 + GSE16728, DE + concordance
- scripts/week1_finalize.py: mygene ID mapping + persist signature
- tests/test_disease.py: synthetic-data tests for DE/collapse/concordance
- docs/data_sources.md: chosen datasets, group defs, reproduction steps
Result: sickle_cell_signature_v1.json (gitignored), Tier A, 250 up /
227 down genes from 671 concordant (GSE35007 Illumina whole blood SS/AA +
GSE16728 Affymetrix whole blood patient/control). Documented caveats:
missing HbF axis (globin depletion) and reticulocyte composition confound.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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2026-06-23 20:43:54 +02:00 |
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b731478f5d
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Scaffold Reverso MVP pipeline structure
Set up the project skeleton per PLAN.md §4:
- src/ package: identifiers, disease, drugs, scoring, provenance
with pydantic schemas and confidence-tier logic (working);
data-pull/compute functions stubbed per their build week
- 5 starter notebooks (01-05) with PLAN-referenced steps
- tests/test_scoring.py: tier-assignment tests pass; scoring
reference test xfail until Week 3
- docs/: recovery_test_report, data_sources, known_limitations skeletons
- pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README
- data/ tree preserved via .gitkeep; raw/processed/results gitignored
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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2026-06-23 20:20:09 +02:00 |
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