Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
ToolUniverse workflow — Gwas Trait To Gene. An agent skill from lamm-mit/scienceclaw.
$ npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install lamm-mit/scienceclaw gwas-trait-to-gene --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/gwas-trait-to-gene .claude/skills/gwas-trait-to-gene && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "gwas-trait-to-gene" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/gwas-trait-to-gene into .claude/skills/gwas-trait-to-gene/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-trait-to-gene", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/lamm-mit/scienceclaw/tree/main/skills/gwas-trait-to-geneType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install lamm-mit/scienceclaw gwas-trait-to-gene --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/gwas-trait-to-gene .agents/skills/gwas-trait-to-gene && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "gwas-trait-to-gene" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/gwas-trait-to-gene into .agents/skills/gwas-trait-to-gene/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-trait-to-gene", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install lamm-mit/scienceclaw gwas-trait-to-gene --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/gwas-trait-to-gene .cursor/skills/gwas-trait-to-gene && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "gwas-trait-to-gene" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/gwas-trait-to-gene into .cursor/skills/gwas-trait-to-gene/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-trait-to-gene", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/lamm-mit/scienceclaw.git --path skills/gwas-trait-to-gene--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install lamm-mit/scienceclaw gwas-trait-to-gene --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/gwas-trait-to-gene .gemini/skills/gwas-trait-to-gene && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "gwas-trait-to-gene" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/gwas-trait-to-gene into .gemini/skills/gwas-trait-to-gene/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-trait-to-gene", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install lamm-mit/scienceclaw gwas-trait-to-geneInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/gwas-trait-to-gene .github/skills/gwas-trait-to-gene && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "gwas-trait-to-gene" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/gwas-trait-to-gene into .github/skills/gwas-trait-to-gene/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-trait-to-gene", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install lamm-mit/scienceclaw gwas-trait-to-gene --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/gwas-trait-to-gene .opencode/skills/gwas-trait-to-gene && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "gwas-trait-to-gene" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/gwas-trait-to-gene into .opencode/skills/gwas-trait-to-gene/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-trait-to-gene", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
gwas-trait-to-geneToolUniverse workflow — Gwas Trait To Gene. An agent skill from lamm-mit/scienceclaw.
Gwas Trait To Gene is an agent skill from lamm-mit/scienceclaw. ToolUniverse workflow — Gwas Trait To Gene
Its SKILL.md is about 2.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts (for example `scripts/run.py`).
It sits in Research & Science. The licence is Apache-2.0.
4 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit ab9aba1. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Ships 2 files in scripts/ (Python), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Links to these hosts (documentation or services it may open):
ebi.ac.ukgenetics.opentargets.orgFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Gwas Trait To Gene loads about 2.2k tokens when it runs. Until then it costs about 15 tokens; SKILL.md has 710 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
The full file from lamm-mit/scienceclaw at commit ab9aba1, republished under its Apache-2.0 licence (© lamm-mit). 710 words, ~2,220 tokens.
.claude/skills/gwas-trait-to-gene/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.Discover genes associated with diseases and traits using genome-wide association studies (GWAS)
This skill enables systematic discovery of genes linked to diseases/traits by analyzing GWAS data from two major resources:
Clinical Research
Drug Target Discovery
Functional Genomics
1. Trait Search → Search GWAS Catalog by disease/trait name
↓
2. SNP Aggregation → Collect genome-wide significant SNPs (p < 5e-8)
↓
3. Gene Mapping → Extract mapped genes from associations
↓
4. Evidence Ranking → Score by p-value, replication, fine-mapping
↓
5. Annotation (Optional) → Add L2G predictions from Open TargetsGenome-wide Significance
Gene Mapping Methods
Evidence Confidence Levels
gwas_get_associations_for_trait - Get all associations for a trait (sorted by p-value)gwas_search_snps - Search SNPs by gene mappinggwas_get_snp_by_id - Get SNP details (MAF, consequence, location)gwas_get_study_by_id - Get study metadatagwas_search_associations - Search associations with filtersgwas_search_studies - Search studies by trait/cohortgwas_get_associations_for_snp - Get all associations for a SNPgwas_get_variants_for_trait - Get variants for a traitgwas_get_studies_for_trait - Get studies for a traitgwas_get_snps_for_gene - Get SNPs mapped to a genegwas_get_associations_for_study - Get associations from a studyOpenTargets_search_gwas_studies_by_disease - Search studies by disease ontologyOpenTargets_get_study_credible_sets - Get fine-mapped loci for a studyOpenTargets_get_variant_credible_sets - Get credible sets for a variantOpenTargets_get_variant_info - Get variant annotation (frequencies, consequences)OpenTargets_get_gwas_study - Get study metadataOpenTargets_get_credible_set_detail - Get detailed credible set informationRequired
trait - Disease/trait name (e.g., "type 2 diabetes", "coronary artery disease")Optional
p_value_threshold - Significance threshold (default: 5e-8)min_evidence_count - Minimum number of studies (default: 1)max_results - Maximum genes to return (default: 100)use_fine_mapping - Include L2G predictions (default: true)disease_ontology_id - Disease ontology ID for Open Targets (e.g., "MONDO_0005148"){
"genes": [
{
"symbol": str, # Gene symbol (e.g., "TCF7L2")
"min_p_value": float, # Most significant p-value
"evidence_count": int, # Number of independent studies
"snps": [str], # Associated SNP rs IDs
"studies": [str], # GWAS study accessions
"l2g_score": float | null, # Locus-to-gene score (0-1)
"credible_sets": int, # Number of credible sets
"confidence_level": str # "High", "Medium", or "Low"
}
],
"summary": {
"trait": str,
"total_associations": int,
"significant_genes": int,
"data_sources": ["GWAS Catalog", "Open Targets"]
}
}Type 2 Diabetes
TCF7L2: p=1.2e-98, 15 studies, L2G=0.82 → High confidence
KCNJ11: p=3.4e-67, 12 studies, L2G=0.76 → High confidence
PPARG: p=2.1e-45, 8 studies, L2G=0.71 → High confidence
FTO: p=5.6e-42, 10 studies, L2G=0.68 → High confidence
IRS1: p=8.9e-38, 6 studies, L2G=0.54 → High confidenceAlzheimer's Disease
APOE: p=1.0e-450, 25 studies, L2G=0.95 → High confidence
BIN1: p=2.3e-89, 18 studies, L2G=0.88 → High confidence
CLU: p=4.5e-67, 16 studies, L2G=0.82 → High confidence
ABCA7: p=6.7e-54, 14 studies, L2G=0.79 → High confidence
CR1: p=8.9e-52, 13 studies, L2G=0.75 → High confidence1. Use Disease Ontology IDs for Precision
# Instead of:
discover_gwas_genes("diabetes") # Ambiguous
# Use:
discover_gwas_genes(
"type 2 diabetes",
disease_ontology_id="MONDO_0005148" # Specific
)2. Filter by Evidence Strength
# For drug targets, require strong evidence:
discover_gwas_genes(
"coronary artery disease",
p_value_threshold=5e-10, # Stricter than GWAS threshold
min_evidence_count=3, # Multiple independent studies
use_fine_mapping=True # Include L2G predictions
)3. Interpret Results Carefully
Gene Mapping Uncertainty
Population Bias
Sample Size Dependence
Validation Bug
validate=False parameter if neededGWAS Catalog
Open Targets Genetics
If you use this skill in research, please cite:
Buniello A, et al. (2019) The NHGRI-EBI GWAS Catalog of published genome-wide
association studies. Nucleic Acids Research, 47(D1):D1005-D1012.
Mountjoy E, et al. (2021) An open approach to systematically prioritize causal
variants and genes at all published human GWAS trait-associated loci.
Nature Genetics, 53:1527-1533.For issues with:
© lamm-mit, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 2 other files (scripts) in skills/gwas-trait-to-gene of lamm-mit/scienceclaw.
Open the folder on GitHubat commit ab9aba1
Gwas Trait To Gene next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Gwas Trait To Gene this skilllamm-mit/scienceclaw | 246 | — | ~2.2k | Automated safety check: Pass | Apache-2.0 | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Last30daysmvanhorn/last30days-skill | 64k | — | ~7.9k | Automated safety check: Notes | MIT |
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
mvanhorn/last30days-skill
Research what people actually say about any topic in the last 30 days.
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
lamm-mit/scienceclaw
Query FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources.
lamm-mit/scienceclaw
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections.
lamm-mit/scienceclaw
Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index.
lamm-mit/scienceclaw
Cloud-based quantum chemistry platform with Python API. An agent skill from lamm-mit/scienceclaw.
lamm-mit/scienceclaw
Create professional infographics using Nano Banana Pro AI with smart iterative refinement.
lamm-mit/scienceclaw
Generate comprehensive disease research reports using 100+ ToolUniverse tools.
Categories
ToolUniverse workflow — Gwas Trait To Gene. An agent skill from lamm-mit/scienceclaw. Gwas Trait To Gene is an agent skill from lamm-mit/scienceclaw.
Gwas Trait To Gene fits situations like: research & Science work in your project.
Run `npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a claude-code`. Or copy the skill folder (skills/gwas-trait-to-gene in lamm-mit/scienceclaw) into .claude/skills/gwas-trait-to-gene in your project. Claude Code loads it when a task matches its description.
Run `npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a codex`. Or copy the skill folder (skills/gwas-trait-to-gene in lamm-mit/scienceclaw) into .agents/skills/gwas-trait-to-gene in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add lamm-mit/scienceclaw --skill gwas-trait-to-gene -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gwas-trait-to-gene, .gemini/skills/gwas-trait-to-gene, .github/skills/gwas-trait-to-gene and .opencode/skills/gwas-trait-to-gene in your project.
Going by SKILL.md and its folder, Gwas Trait To Gene needs Python for the scripts in its folder. Our summary lists: Python 3.
SKILL.md names 2 domains. As links in the text: ebi.ac.uk and genetics.opentargets.org. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
Gwas Trait To Gene is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.2k tokens (SKILL.md is roughly 8.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Gwas Trait To Gene: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 246 GitHub stars. The repository holds 86 skills in this directory. The repository was last updated on August 21, 2026.
Source: lamm-mit/scienceclaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.