AA
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数据与复现
CL
claw-ancestry-pca
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Ancestry decomposition PCA against the Simons Genome Diversity Project.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/claw-ancestry-pca
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Place your study cohort in global genetic context by computing joint PCA against Simons Genome Diversity Project (SGDP) — 345 samples ，面向 164 populations spanning every inhabited continent。
- Panel：PC1 vs PC2 — main population structure of your cohort。
- Panel B：PC3 vs PC2 ，支持 regional groupings 、 confidence ellipses。
- Panel C：PC3 vs PC1 ，支持 language/cultural groupings。
- Panel D：Global context — your samples (circles) vs SGDP (triangles)。
原始文档
SKILL.md 摘录
Why this exists
If you ask ChatGPT to "run a PCA against a global reference panel," it will:
- Not know which reference panel to use
- Hallucinate PLINK flags for merging datasets with different variant sets
- Skip IBD removal (related individuals distort PCA)
- Not normalise contig names between your VCF and the reference
- Produce a single scatter plot with no population labels
This skill encodes the correct methodological decisions:
- Uses SGDP (the gold-standard reference for global diversity)
- Handles contig normalisation (chr1 vs 1)
- Filters to common biallelic SNPs shared between datasets
- Removes related individuals via IBD checks
- Produces publication-quality multi-panel figures with confidence ellipses
- Differentiates your samples (circles) from reference (triangles)
Reference Panel
The skill bundles the SGDP v4 dataset (Mallick et al., 2016, Nature):
- 345 samples from 164 populations
- Whole-genome sequencing at high coverage
- MAF > 0.1% filter applied
- Populations span: Africa, Americas, Central/South Asia, East Asia, Europe, Middle East, Oceania
Demo (works out of the box)
The demo uses pre-computed PCA results from the Peruvian Genome Project (736 samples, 28 populations) and generates the full 4-panel figure instantly.
适用场景
- Use claw-ancestry-pca ，用于 medicinal chemistry 、 drug-discovery work。
- Apply claw-ancestry-pca to compound，target，或 screening workflows。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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