bio-causal-genomics-transcriptome-wide-association skillA
bio-causal-genomics-transcriptome-wide-association is agent-read markdown (skill) from pku-yuangroup/openai4s: Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-MultiXcan, UTMOST, MOSTWAS, kTWAS, EpiXcan, TIGAR-V2, and probabilistic fine-mapping with FOCUS and MA-FOCUS. Use when running TWAS from GWAS sumstats, prioritising candidate causal genes from a GWAS lead locus, picking single-tissue vs cross-tissue models, identifying LD-induced TWAS false positives, choosing ancestry-matched prediction weights, fine-m.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility Reference examples tested with: FUSION (head of `gusevlab/fusion_twas`, scripts dated 2023+), MetaXcan / S-PrediXcan / S-MultiXcan 0.7.5+ (`hakyimlab/MetaXcan`), PrediXcan model files from PredictDB (GTEx v8 elastic-net + MASHR), UTMOST (head of `Joker-Jerome/UTMOST`), pyfocus 0.8+ (`bogdanlab/focus`), MA-FOCUS (head of `mancusolab/ma-focus`), TIGAR-V2 (head of `yanglab-emory/TIGAR`), PLINK 1.9 + PLINK 2.0, R 4.3+, Python 3.9-3.11. Before using code patterns, verify installed versions match. If versions differ: - R: `Rscript --version`; for FUSION scripts inspect `--help` flags directly in the source - Python: `pip show pyfocus` (MetaXcan is git-cloned, not on PyPI) then `SPrediXcan.py --help`, `SMulTiXcan.py --help`, `focus finemap --help` - CLI: `plink2 --version`; FUSION ships as R scripts not a binary If a script throws an error about an argument that has moved (e.g. `--gwas_file` vs `--gwas-file`) or a model database schema change, introspect the installed script with `--help` and adapt rather than retrying. PredictDB model file paths change with GTEx version; pin the version explicitly in scripts. # Transcriptome-Wide Association …
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How to install
mdr add pku-yuangroup/openai4s/bio-causal-genomics-transcriptome-wide-association@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-causal-genomics-transcriptome-wide-association@sha256:0a032ddd49e2c5d6Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Audit of the latest version
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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