MFA Pipeline Orchestrator
aiming-lab/AutoResearchClaw
Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
Automate gene expression analysis with the GenoMAS multi-agent system
Install Genomas Guide
$ npx skills add wentorai/research-plugins --skill genomas-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins genomas-guide --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/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/domains/biomedical/genomas-guide .claude/skills/genomas-guide && 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 "genomas-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genomas-guide into .claude/skills/genomas-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomas-guide", 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/wentorai/research-plugins/tree/main/skills/domains/biomedical/genomas-guideType 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 wentorai/research-plugins --skill genomas-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins genomas-guide --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/domains/biomedical/genomas-guide .agents/skills/genomas-guide && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "genomas-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genomas-guide into .agents/skills/genomas-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomas-guide", 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 wentorai/research-plugins --skill genomas-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins genomas-guide --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/domains/biomedical/genomas-guide .cursor/skills/genomas-guide && 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 "genomas-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genomas-guide into .cursor/skills/genomas-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomas-guide", 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/wentorai/research-plugins.git --path skills/domains/biomedical/genomas-guide--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 wentorai/research-plugins --skill genomas-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins genomas-guide --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/domains/biomedical/genomas-guide .gemini/skills/genomas-guide && 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 "genomas-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genomas-guide into .gemini/skills/genomas-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomas-guide", 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 wentorai/research-plugins genomas-guideInstalls 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 wentorai/research-plugins --skill genomas-guide -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/domains/biomedical/genomas-guide .github/skills/genomas-guide && 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 "genomas-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genomas-guide into .github/skills/genomas-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomas-guide", 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 wentorai/research-plugins --skill genomas-guide -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install wentorai/research-plugins genomas-guide --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/domains/biomedical/genomas-guide .opencode/skills/genomas-guide && 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 "genomas-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genomas-guide into .opencode/skills/genomas-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomas-guide", 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
genomas-guide- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~958 tokens
- SKILL.md length
- 182 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
Automate gene expression analysis with the GenoMAS multi-agent system
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, Installation, Core Workflow and Supported Analyses, plus 2 more sections
- Calls pip and git; reaches github.com
- Tasks that involve Multi-agent orchestration
What it does
Genomas Guide is an agent skill from wentorai/research-plugins. Automate gene expression analysis with the GenoMAS multi-agent system
Its SKILL.md is about 960 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics and Multi-agent orchestration. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve Multi-agent orchestration
Example prompts
- “/genomas-guide”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit bf44b3c. 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
Shell commands in SKILL.md call:
pipgit
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:
github.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
Genomas Guide loads about 958 tokens when it runs. Until then it costs about 21 tokens; SKILL.md has 182 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
The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 182 words, ~958 tokens.
Download SKILL.mdSave it as
.claude/skills/genomas-guide/SKILL.md (or your agent's skills folder).- name
- genomas-guide
- description
- Automate gene expression analysis with the GenoMAS multi-agent system
GenoMAS Guide
Overview
GenoMAS (Genomics Multi-Agent System) is a minimalist multi-agent framework for automating scientific analysis workflows, particularly gene expression analysis. It orchestrates specialized agents for data retrieval, preprocessing, differential expression analysis, pathway enrichment, and visualization — turning a natural language research question into a complete bioinformatics pipeline.
Installation
pip install genomas
# Or from source
git clone https://github.com/futianfan/GenoMAS.git
cd GenoMAS && pip install -e .Core Workflow
Natural Language to Pipeline
from genomas import GenoMAS
geno = GenoMAS(llm_provider="anthropic")
# Describe analysis in natural language
result = geno.analyze(
"Compare gene expression between tumor and normal tissue "
"in the TCGA breast cancer dataset. Identify differentially "
"expressed genes and run pathway enrichment analysis."
)
# GenoMAS automatically:
# 1. Retrieves TCGA-BRCA data via GDC API
# 2. Normalizes and filters expression data
# 3. Runs DESeq2-style differential expression
# 4. Performs GO and KEGG pathway enrichment
# 5. Generates volcano plots and heatmapsAgent Roles
| Agent | Responsibility |
|---|---|
| Data Agent | Retrieves datasets from GEO, TCGA, ArrayExpress |
| Preprocessing Agent | Quality control, normalization, filtering |
| Analysis Agent | Differential expression, clustering, PCA |
| Enrichment Agent | GO, KEGG, MSigDB pathway analysis |
| Visualization Agent | Plots, heatmaps, volcano plots |
| Report Agent | Generates methods section and results summary |
Step-by-Step Usage
from genomas import DataAgent, AnalysisAgent, EnrichmentAgent
# Step 1: Retrieve data
data_agent = DataAgent()
dataset = data_agent.fetch("GSE12345", platform="RNA-seq")
# Step 2: Differential expression
analysis = AnalysisAgent()
de_results = analysis.differential_expression(
dataset,
group_col="condition",
case="tumor",
control="normal",
method="deseq2",
)
# Step 3: Filter significant genes
sig_genes = de_results[
(de_results["padj"] < 0.05) &
(abs(de_results["log2FoldChange"]) > 1)
]
print(f"Found {len(sig_genes)} differentially expressed genes")
# Step 4: Pathway enrichment
enrichment = EnrichmentAgent()
pathways = enrichment.run(
gene_list=sig_genes["gene_symbol"].tolist(),
databases=["GO_BP", "KEGG", "Reactome"],
)
# Step 5: Visualize
from genomas.viz import volcano_plot, pathway_barplot
volcano_plot(de_results, output="volcano.png")
pathway_barplot(pathways, top_n=20, output="pathways.png")Supported Analyses
| Analysis | Method |
|---|---|
| Differential expression | DESeq2, edgeR, limma-voom |
| Clustering | Hierarchical, k-means, UMAP |
| PCA | Principal component analysis |
| GO enrichment | Gene Ontology term enrichment |
| KEGG pathway | KEGG pathway mapping |
| GSEA | Gene Set Enrichment Analysis |
| Survival analysis | Kaplan-Meier, Cox regression |
Data Sources
| Source | Data type |
|---|---|
| GEO (NCBI) | Microarray, RNA-seq |
| TCGA | Cancer genomics |
| GTEx | Normal tissue expression |
| ArrayExpress | European expression data |
References
- GenoMAS GitHub
- Love, M.I. et al. (2014). "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2." Genome Biology 15(12).
© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/domains/biomedical/genomas-guide of wentorai/research-plugins.
Open the folder on GitHubat commit bf44b3c
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Genomas Guide 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 |
|---|---|---|---|---|---|---|
| Genomas Guide this skillwentorai/research-plugins | 298 | 1 repos | ~958 | Automated safety check: Pass | MIT | |
| MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw | 15k | — | ~923 | Automated safety check: Pass | MIT | |
| ULW Deep Researchcode-yeongyu/oh-my-openagent | 70k | — | ~14k | Automated safety check: Pass | Custom licence | |
| Deep ResearchXiaomiMiMo/MiMo-Code | 14k | — | ~1.2k | Automated safety check: Pass | MIT | |
| Mcpmed Bioinformatics ServerFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~353 | Automated safety check: Pass | MIT | |
| Spatial TrajectoryTianGzlab/OmicsClaw | 161 | — | ~1.3k | Automated safety check: Pass | Apache-2.0 |
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Deep Research
XiaomiMiMo/MiMo-Code
Runs a multi-source investigation with parallel sub-agents and built-in web tools, then writes one cited report. Meant for open-ended topics, not quick lookups.
Mcpmed Bioinformatics Server
FreedomIntelligence/OpenClaw-Medical-Skills
Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.
Spatial Trajectory
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Load when inferring pseudotime / lineage trajectories on a preprocessed spatial AnnData via DPT (default — diffusion pseudotime), CellRank (terminal-state + fate-probability), or Palantir (waypoint…
Kegg Analysis
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Related
Categories
Questions about Genomas Guide
What does Genomas Guide do?
Automate gene expression analysis with the GenoMAS multi-agent system. Genomas Guide is an agent skill from wentorai/research-plugins.
When should I use Genomas Guide?
Genomas Guide fits situations like: tasks that involve Bioinformatics; tasks that involve Multi-agent orchestration.
How do I install Genomas Guide in Claude Code?
Run `npx skills add wentorai/research-plugins --skill genomas-guide -a claude-code`. Or copy the skill folder (skills/domains/biomedical/genomas-guide in wentorai/research-plugins) into .claude/skills/genomas-guide in your project. Claude Code loads it when a task matches its description.
How do I install Genomas Guide in Codex?
Run `npx skills add wentorai/research-plugins --skill genomas-guide -a codex`. Or copy the skill folder (skills/domains/biomedical/genomas-guide in wentorai/research-plugins) into .agents/skills/genomas-guide in your project. Codex loads it when a task matches its description.
Can I use Genomas Guide 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 wentorai/research-plugins --skill genomas-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/genomas-guide, .gemini/skills/genomas-guide, .github/skills/genomas-guide and .opencode/skills/genomas-guide in your project.
What does Genomas Guide need to run?
Going by SKILL.md and its folder, Genomas Guide needs the command-line tools its instructions call (pip and git). Our summary lists: Python 3.
Does Genomas Guide access the network?
SKILL.md names 1 domain. In commands or code: github.com; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.
Is Genomas Guide 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 Genomas Guide use?
Genomas Guide is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Genomas Guide use?
About 958 tokens (SKILL.md is roughly 3.8k 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 Genomas Guide?
Skills that share tags, products or a category with Genomas Guide: MFA Pipeline Orchestrator (aiming-lab/AutoResearchClaw, 15k stars), ULW Deep Research (code-yeongyu/oh-my-openagent, 70k stars), Deep Research (XiaomiMiMo/MiMo-Code, 14k stars) and Mcpmed Bioinformatics Server (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Genomas Guide?
wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.
Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.