Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Agent skill
Bio Causal Genomics Fine Mapping
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search.
Install Bio Causal Genomics Fine Mapping
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-causal-genomics-fine-mapping --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-causal-genomics-fine-mapping .claude/skills/bio-causal-genomics-fine-mapping && 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 "bio-causal-genomics-fine-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-causal-genomics-fine-mapping into .claude/skills/bio-causal-genomics-fine-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-causal-genomics-fine-mapping", 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/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-causal-genomics-fine-mappingType 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-causal-genomics-fine-mapping --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-causal-genomics-fine-mapping .agents/skills/bio-causal-genomics-fine-mapping && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-causal-genomics-fine-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-causal-genomics-fine-mapping into .agents/skills/bio-causal-genomics-fine-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-causal-genomics-fine-mapping", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-causal-genomics-fine-mapping --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-causal-genomics-fine-mapping .cursor/skills/bio-causal-genomics-fine-mapping && 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 "bio-causal-genomics-fine-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-causal-genomics-fine-mapping into .cursor/skills/bio-causal-genomics-fine-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-causal-genomics-fine-mapping", 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/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-causal-genomics-fine-mapping--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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-causal-genomics-fine-mapping --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-causal-genomics-fine-mapping .gemini/skills/bio-causal-genomics-fine-mapping && 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 "bio-causal-genomics-fine-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-causal-genomics-fine-mapping into .gemini/skills/bio-causal-genomics-fine-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-causal-genomics-fine-mapping", 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 FreedomIntelligence/OpenClaw-Medical-Skills bio-causal-genomics-fine-mappingInstalls 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-causal-genomics-fine-mapping .github/skills/bio-causal-genomics-fine-mapping && 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 "bio-causal-genomics-fine-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-causal-genomics-fine-mapping into .github/skills/bio-causal-genomics-fine-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-causal-genomics-fine-mapping", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-causal-genomics-fine-mapping --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-causal-genomics-fine-mapping .opencode/skills/bio-causal-genomics-fine-mapping && 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 "bio-causal-genomics-fine-mapping" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-causal-genomics-fine-mapping into .opencode/skills/bio-causal-genomics-fine-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-causal-genomics-fine-mapping", 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.
Facts
- Skill name
bio-causal-genomics-fine-mapping- GitHub stars
- 3.1k
- Token cost
- ~2.3k tokens
- SKILL.md length
- 319 words
- Files
- 5
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search.
- Narrowing GWAS association signals to candidate causal variants
- SKILL.md covers Version Compatibility, Overview, SuSiE (Sum of Single Effects) and SuSiE with Summary Statistics…, plus 6 more sections
- Runs R and Shell scripts from its folder; reaches christianbenner.com
- Building credible sets for functional validation
What it does
Bio Causal Genomics Fine Mapping is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.
Its SKILL.md is about 2.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files (for example `examples/finemap_pipeline.sh` and `usage-guide.md`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Narrowing GWAS association signals to candidate causal variants
- Building credible sets for functional validation
Example prompts
- “/bio-causal-genomics-fine-mapping”
Requirements
- A Bash shell
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.
Tool permissions
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.
Runs code
Ships script files (R and Shell), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
christianbenner.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Bio Causal Genomics Fine Mapping loads about 2.3k tokens when it runs. Until then it costs about 102 tokens; SKILL.md has 319 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.
Safety
Auto-check passed
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); files beside SKILL.md are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 319 words (~2,309 tokens).
“Reference examples tested with: ggplot2 3.5+”
- name
- bio-causal-genomics-fine-mapping
- tool_type
- r
- primary_tool
- susieR
Files
SKILL.md and 4 other files in skills/bio-causal-genomics-fine-mapping of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/finemap_pipeline.sh
- examples/pip_visualization.R
- examples/susie_finemapping.R
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Compare with similar skills
Bio Causal Genomics Fine Mapping 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 |
|---|---|---|---|---|---|---|
| Bio Causal Genomics Fine Mapping this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~2.3k | Automated safety check: Pass | None | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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Clinvar Database
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
Metabolic Study Planner
aiming-lab/AutoResearchClaw
Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
MFA Pipeline Orchestrator
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Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
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Related
Categories
Questions about Bio Causal Genomics Fine Mapping
What does Bio Causal Genomics Fine Mapping do?
Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Bio Causal Genomics Fine Mapping is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search.
When should I use Bio Causal Genomics Fine Mapping?
Bio Causal Genomics Fine Mapping fits situations like: narrowing GWAS association signals to candidate causal variants; building credible sets for functional validation.
How do I install Bio Causal Genomics Fine Mapping in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a claude-code`. Or copy the skill folder (skills/bio-causal-genomics-fine-mapping in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-causal-genomics-fine-mapping in your project. Claude Code loads it when a task matches its description.
How do I install Bio Causal Genomics Fine Mapping in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a codex`. Or copy the skill folder (skills/bio-causal-genomics-fine-mapping in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-causal-genomics-fine-mapping in your project. Codex loads it when a task matches its description.
Can I use Bio Causal Genomics Fine Mapping in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-causal-genomics-fine-mapping -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-causal-genomics-fine-mapping, .gemini/skills/bio-causal-genomics-fine-mapping, .github/skills/bio-causal-genomics-fine-mapping and .opencode/skills/bio-causal-genomics-fine-mapping in your project.
What does Bio Causal Genomics Fine Mapping need to run?
Going by SKILL.md and its folder, Bio Causal Genomics Fine Mapping needs R and a shell for the scripts in its folder. Our summary lists: A Bash shell.
Does Bio Causal Genomics Fine Mapping access the network?
SKILL.md names 1 domain. In commands or code: christianbenner.com; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.
Is Bio Causal Genomics Fine Mapping safe to install?
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. Review the folder before installing.
What licence does Bio Causal Genomics Fine Mapping use?
No licence was found for Bio Causal Genomics Fine Mapping or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Causal Genomics Fine Mapping use?
About 2.3k tokens (SKILL.md is roughly 9.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Bio Causal Genomics Fine Mapping?
Skills that share tags, products or a category with Bio Causal Genomics Fine Mapping: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Causal Genomics Fine Mapping?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 GitHub stars. The repository holds 279 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.