Guardat en:
| Autor principal: | |
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| Format: | Recurso digital |
| Idioma: | anglès |
| Publicat: |
Zenodo
2025
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| Matèries: | |
| Accés en línia: | https://doi.org/10.5281/zenodo.17799514 |
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Taula de continguts:
- This repository contains the code, configuration, and reproducibility artifacts for the paper "Path-Probability Models Outperform Point-Estimate Scores for Noncoding GWAS Gene Prioritization". The framework implements probabilistic mechanism graphs with path-probability inference for GWAS gene prioritization, demonstrating that explicit causal paths outperform point-estimate locus-to-gene scores. Key features: - SuSiE-based fine-mapping with multi-signal support - coloc.susie colocalization for multi-causal variant handling - ABC (Activity-by-Contact) and PCHi-C enhancer-gene linking - Noisy-OR probabilistic inference model - Per-module probability calibration (ECE < 0.05) - eQTL Catalogue cross-study replication (78% replication rate) - Three-tier benchmark system with anti-leakage provisions Results: - 76% recall at rank 20 vs 58% for Open Targets L2G - Effect size correlation r=0.89 with eQTL Catalogue - Calibrated probabilities at each module Full pipeline reproducible via Snakemake workflow.