Agent skill

Genotex Benchmark Guide

by wentorai in wentorai/research-plugins

Benchmark for LLM agents on gene expression data analysis. An agent skill from wentorai/research-plugins.

Install Genotex Benchmark Guide

skills CLI

$ npx skills add wentorai/research-plugins --skill genotex-benchmark-guide -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins genotex-benchmark-guide --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/domains/biomedical/genotex-benchmark-guide .claude/skills/genotex-benchmark-guide && rm -rf skills-src

Use ~/.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/

Paste into Claude Code

Install the "genotex-benchmark-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genotex-benchmark-guide into .claude/skills/genotex-benchmark-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genotex-benchmark-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

$skill-installer install https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genotex-benchmark-guide

Type 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.

skills CLI

$ npx skills add wentorai/research-plugins --skill genotex-benchmark-guide -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins genotex-benchmark-guide --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/domains/biomedical/genotex-benchmark-guide .agents/skills/genotex-benchmark-guide && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "genotex-benchmark-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genotex-benchmark-guide into .agents/skills/genotex-benchmark-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genotex-benchmark-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.

skills CLI

$ npx skills add wentorai/research-plugins --skill genotex-benchmark-guide -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins genotex-benchmark-guide --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/domains/biomedical/genotex-benchmark-guide .cursor/skills/genotex-benchmark-guide && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "genotex-benchmark-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genotex-benchmark-guide into .cursor/skills/genotex-benchmark-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genotex-benchmark-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

$ gemini skills install https://github.com/wentorai/research-plugins.git --path skills/domains/biomedical/genotex-benchmark-guide

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add wentorai/research-plugins --skill genotex-benchmark-guide -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins genotex-benchmark-guide --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/domains/biomedical/genotex-benchmark-guide .gemini/skills/genotex-benchmark-guide && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "genotex-benchmark-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genotex-benchmark-guide into .gemini/skills/genotex-benchmark-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genotex-benchmark-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.

GitHub CLI

$ gh skill install wentorai/research-plugins genotex-benchmark-guide

Installs 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).

skills CLI

$ npx skills add wentorai/research-plugins --skill genotex-benchmark-guide -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/domains/biomedical/genotex-benchmark-guide .github/skills/genotex-benchmark-guide && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "genotex-benchmark-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genotex-benchmark-guide into .github/skills/genotex-benchmark-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genotex-benchmark-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.

skills CLI

$ npx skills add wentorai/research-plugins --skill genotex-benchmark-guide -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins genotex-benchmark-guide --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/domains/biomedical/genotex-benchmark-guide .opencode/skills/genotex-benchmark-guide && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "genotex-benchmark-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/genotex-benchmark-guide into .opencode/skills/genotex-benchmark-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genotex-benchmark-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: genotex-benchmark-guide
GitHub stars: 298
Used in: 1 other repo
Token cost: ~956 tokens
SKILL.md length: 106 words
Files: 1
Skills in repo: 405
Repo updated: Jun 19, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Benchmark for LLM agents on gene expression data analysis. An agent skill from wentorai/research-plugins.

Works in 5 steps: Agent evaluation: Test bioinformatics… → Method comparison: Compare LLM agents on… → Benchmark development: Extend with new… → …
Tasks that involve Bioinformatics
SKILL.md covers Overview, Benchmark Structure, Usage and Running Evaluations, plus 3 more sections
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Genotex Benchmark Guide is an agent skill from wentorai/research-plugins. Benchmark for LLM agents on gene expression data analysis

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 Data & Analytics, covering Bioinformatics and Data analysis. 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 Data analysis

Example prompts

“/genotex-benchmark-guide”

Requirements

Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

Agent evaluation: Test bioinformatics agents on real tasks
Method comparison: Compare LLM agents on genomics
Benchmark development: Extend with new GEO datasets
Teaching: Standard tasks for bioinformatics education
Tool development: Test new analysis pipelines

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
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- github.com
- ncbi.nlm.nih.gov
- mlcb.github.io
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

Genotex Benchmark Guide loads about 956 tokens when it runs. Until then it costs about 20 tokens; SKILL.md has 106 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~20
When it runs · the whole SKILL.md, loaded when a task matches: ~956

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). 106 words, ~956 tokens.

Download SKILL.mdSave it as .claude/skills/genotex-benchmark-guide/SKILL.md (or your agent's skills folder).

name: genotex-benchmark-guide
description: Benchmark for LLM agents on gene expression data analysis

GenoTEX Benchmark Guide

Overview

GenoTEX is a benchmark for evaluating LLM-based agents on gene expression data analysis tasks. It provides curated datasets from GEO (Gene Expression Omnibus) with ground-truth analysis pipelines, testing agents on data preprocessing, differential expression, enrichment analysis, and biological interpretation. Published at MLCB 2025 as an oral presentation.

Benchmark Structure

GenoTEX Benchmark
├── Data Collection
│   └── Curated GEO datasets with ground truth
├── Task Categories
│   ├── Data preprocessing (QC, normalization)
│   ├── Differential expression analysis
│   ├── Gene set enrichment analysis
│   ├── Clustering and classification
│   └── Biological interpretation
├── Evaluation
│   ├── Code correctness (executes without error)
│   ├── Statistical validity (appropriate tests)
│   ├── Result accuracy (vs ground truth)
│   └── Interpretation quality (biological insight)
└── Baselines
    ├── GPT-4 agent
    ├── Claude agent
    └── Domain-specific fine-tuned models

Usage

python

from genotex import GenoTEXBenchmark

bench = GenoTEXBenchmark()

# List available tasks
tasks = bench.list_tasks()
for task in tasks[:5]:
    print(f"Task: {task.id}")
    print(f"  Dataset: {task.geo_accession}")
    print(f"  Category: {task.category}")
    print(f"  Difficulty: {task.difficulty}")

# Get a specific task
task = bench.get_task("GSE12345_DEG")
print(f"Description: {task.description}")
print(f"Input files: {task.input_files}")
print(f"Expected output: {task.expected_output_type}")

Running Evaluations

python

# Evaluate an agent on GenoTEX
from genotex import evaluate_agent

results = evaluate_agent(
    agent_fn=my_agent_function,
    tasks="all",            # or specific task IDs
    timeout_per_task=300,   # seconds
)

print(f"Tasks completed: {results.completed}/{results.total}")
print(f"Code correctness: {results.code_correct_rate:.1%}")
print(f"Statistical validity: {results.stats_valid_rate:.1%}")
print(f"Result accuracy: {results.accuracy:.3f}")

Task Examples

python

# Example: Differential Expression Analysis
task = {
    "id": "GSE12345_DEG",
    "description": "Identify differentially expressed genes "
                   "between treatment and control groups in "
                   "this RNA-seq dataset.",
    "input": "GSE12345_counts.csv",  # Raw count matrix
    "metadata": "GSE12345_metadata.csv",  # Sample info
    "expected": {
        "method": "DESeq2 or limma-voom",
        "output": "DEG table with log2FC, p-value, adj.p",
        "ground_truth": "GSE12345_deg_truth.csv",
    },
}

# Example: Gene Set Enrichment
task = {
    "id": "GSE12345_GSEA",
    "description": "Perform gene set enrichment analysis on "
                   "the DEGs and identify enriched pathways.",
    "input": "GSE12345_deg_results.csv",
    "expected": {
        "method": "fgsea, clusterProfiler, or enrichR",
        "output": "Enriched pathways with NES and FDR",
    },
}

Use Cases

Agent evaluation: Test bioinformatics agents on real tasks
Method comparison: Compare LLM agents on genomics
Benchmark development: Extend with new GEO datasets
Teaching: Standard tasks for bioinformatics education
Tool development: Test new analysis pipelines

References

Files

Just SKILL.md in skills/domains/biomedical/genotex-benchmark-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.

brycewang-stanford/Auto-Empirical-Research-Skillsskills/43-wentorai-research-plugins/skills/domains/biomedical/genotex-benchmark-guide

Compare with similar skills

Genotex Benchmark 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.

Genotex Benchmark Guide compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Genotex Benchmark Guide this skillwentorai/research-plugins	298	1 repos	~956	Automated safety check: Pass	MIT	3 mo ago
Exploratory Data Analysisspacering-net/codeg	3.9k	14 repos	~3.6k	Automated safety check: Pass	MIT	yesterday
Pyopenmsdavila7/claude-code-templates	32k	11 repos	~1.4k	Automated safety check: Pass	MIT	yesterday
Gwas Databasedavila7/claude-code-templates	32k	10 repos	~5k	Automated safety check: Pass	MIT	yesterday
Bioconductor BiomartbioMate-AI/biomate-bioconductor-kb	804	—	~4.5k	Automated safety check: Pass	Custom licence	3 mo ago
Bio Data Visualization Manhattan Qq LocuszoomGPTomics/bioSkills	1.2k	2 repos	~4.3k	Automated safety check: Pass	MIT	1 mo ago

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Questions about Genotex Benchmark Guide

What does Genotex Benchmark Guide do?

Benchmark for LLM agents on gene expression data analysis. An agent skill from wentorai/research-plugins. Genotex Benchmark Guide is an agent skill from wentorai/research-plugins.

When should I use Genotex Benchmark Guide?

Genotex Benchmark Guide fits situations like: tasks that involve Bioinformatics; tasks that involve Data analysis.

How do I install Genotex Benchmark Guide in Claude Code?

Run `npx skills add wentorai/research-plugins --skill genotex-benchmark-guide -a claude-code`. Or copy the skill folder (skills/domains/biomedical/genotex-benchmark-guide in wentorai/research-plugins) into .claude/skills/genotex-benchmark-guide in your project. Claude Code loads it when a task matches its description.

How do I install Genotex Benchmark Guide in Codex?

Run `npx skills add wentorai/research-plugins --skill genotex-benchmark-guide -a codex`. Or copy the skill folder (skills/domains/biomedical/genotex-benchmark-guide in wentorai/research-plugins) into .agents/skills/genotex-benchmark-guide in your project. Codex loads it when a task matches its description.

Can I use Genotex Benchmark 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 genotex-benchmark-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/genotex-benchmark-guide, .gemini/skills/genotex-benchmark-guide, .github/skills/genotex-benchmark-guide and .opencode/skills/genotex-benchmark-guide in your project.

What does Genotex Benchmark Guide need to run?

SKILL.md names no scripts, command-line tools or credentials: Genotex Benchmark Guide is instructions for the agent only. Our summary lists: Python 3.

Does Genotex Benchmark Guide access the network?

SKILL.md names 3 domains. As links in the text: github.com, ncbi.nlm.nih.gov and mlcb.github.io. This is read from the text; nothing was executed.

Is Genotex Benchmark 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 Genotex Benchmark Guide use?

Genotex Benchmark 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 Genotex Benchmark Guide use?

About 956 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 Genotex Benchmark Guide?

Skills that share tags, products or a category with Genotex Benchmark Guide: Exploratory Data Analysis (spacering-net/codeg, 3.9k stars), Pyopenms (davila7/claude-code-templates, 32k stars), Gwas Database (davila7/claude-code-templates, 32k stars) and Bioconductor Biomart (bioMate-AI/biomate-bioconductor-kb, 804 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Genotex Benchmark 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.

Install Genotex Benchmark Guide

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

GenoTEX Benchmark Guide

Overview

Benchmark Structure

Usage

Running Evaluations

Task Examples

Use Cases

References

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from wentorai/research-plugins

Related

Questions about Genotex Benchmark Guide