Agent skill

Grn Tools

Gene regulatory network workflow guide for transcriptomics and single-cell expression matrices using Arboreto, GRNBoost2, and GENIE3.

Apache-2.0Auto-check passedResearch & Science

Install Grn Tools

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill grn-tools -a claude-code

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

GitHub CLI

$ gh skill install DrugClaw/DrugClaw grn-tools --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/DrugClaw/DrugClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genomics/grn-tools .claude/skills/grn-tools && 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 "grn-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/grn-tools into .claude/skills/grn-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grn-tools", 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/DrugClaw/DrugClaw/tree/main/skills/genomics/grn-tools

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 DrugClaw/DrugClaw --skill grn-tools -a codex

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

GitHub CLI

$ gh skill install DrugClaw/DrugClaw grn-tools --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/genomics/grn-tools .agents/skills/grn-tools && 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 "grn-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/grn-tools into .agents/skills/grn-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grn-tools", 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 DrugClaw/DrugClaw --skill grn-tools -a cursor

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

GitHub CLI

$ gh skill install DrugClaw/DrugClaw grn-tools --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/genomics/grn-tools .cursor/skills/grn-tools && 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 "grn-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/grn-tools into .cursor/skills/grn-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grn-tools", 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/DrugClaw/DrugClaw.git --path skills/genomics/grn-tools

--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 DrugClaw/DrugClaw --skill grn-tools -a gemini-cli

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

GitHub CLI

$ gh skill install DrugClaw/DrugClaw grn-tools --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/DrugClaw/DrugClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/genomics/grn-tools .gemini/skills/grn-tools && 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 "grn-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/grn-tools into .gemini/skills/grn-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grn-tools", 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 DrugClaw/DrugClaw grn-tools

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 DrugClaw/DrugClaw --skill grn-tools -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/genomics/grn-tools .github/skills/grn-tools && 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 "grn-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/grn-tools into .github/skills/grn-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grn-tools", 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 DrugClaw/DrugClaw --skill grn-tools -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 DrugClaw/DrugClaw grn-tools --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/genomics/grn-tools .opencode/skills/grn-tools && 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 "grn-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/genomics/grn-tools into .opencode/skills/grn-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grn-tools", 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: grn-tools
GitHub stars: 126
Token cost: ~692 tokens
SKILL.md length: 236 words
Files: 2
Skills in repo: 25
Repo updated: Mar 23, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Gene regulatory network workflow guide for transcriptomics and single-cell expression matrices using Arboreto, GRNBoost2, and GENIE3.

Works in 5 steps: Confirm the matrix orientation before… → Drop sample-id columns or transpose the… → Provide a TF whitelist when the user… → …
The user asks to infer transcription factor-target links
SKILL.md covers Environment Check, Bundled Asset, Preferred Workflow and Quick Start, plus 2 more sections
Runs Python scripts from its folder; calls python3

What it does

Grn Tools is an agent skill from DrugClaw/DrugClaw. Gene regulatory network workflow guide for transcriptomics and single-cell expression matrices using Arboreto, GRNBoost2, and GENIE3. Use when the user asks to infer transcription factor-target links, score regulatory edges, or build a GRN from bulk or single-cell expression data.

Its SKILL.md is about 690 tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files (for example `templates/arboreto_grn.py`).

It sits in Research & Science, covering Bioinformatics and Transcription. The repository describes itself as: 💊 AI Research Assistant for Accelerated Drug Discovery. 🦞. The licence is Apache-2.0.

When your agent uses it

The user asks to infer transcription factor-target links
Score regulatory edges
Build a GRN from bulk
Single-cell expression data

Example prompts

“/grn-tools”

Requirements

Python 3

Workflow steps

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

Confirm the matrix orientation before inference. Arboreto expects observations as rows and genes as columns.
Drop sample-id columns or transpose the matrix before fitting.
Provide a TF whitelist when the user wants biologically narrower networks.
Save the full ranked edge table and a summary JSON.
Treat the output as an inferred regulatory hypothesis set, not a validated causal network.

What it can do on your machine

Read from SKILL.md and the folder at commit 960a6e0. 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 (Python), which the agent can run.
Shell commands in SKILL.md call:
- python3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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

Grn Tools loads about 692 tokens when it runs. Until then it costs about 73 tokens; SKILL.md has 236 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~73
When it runs · the whole SKILL.md, loaded when a task matches: ~692

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 DrugClaw/DrugClaw at commit 960a6e0, republished under its Apache-2.0 licence (© DrugClaw). 236 words, ~692 tokens.

Download SKILL.mdSave it as .claude/skills/grn-tools/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.

name: grn-tools
description: Gene regulatory network workflow guide for transcriptomics and single-cell expression matrices using Arboreto, GRNBoost2, and GENIE3. Use when the user asks to infer transcription factor-target links, score regulatory edges, or build a GRN from bulk or single-cell expression data.
source: drugclaw
updated_at: 2026-03-11

GRN Tools

Use this skill when the user asks for gene regulatory network inference rather than basic dataset profiling.

Typical triggers:

infer transcription factor to target edges from bulk RNA-seq or single-cell expression data
run GRNBoost2 or GENIE3 on an expression matrix
restrict GRN inference to a curated TF list
export ranked regulatory edges for downstream SCENIC-style or network analysis

Environment Check

bash

which python3 || true
python3 - <<'PY'
mods = ["pandas", "arboreto"]
extra = ["distributed"]
for name in mods + extra:
    try:
        __import__(name)
        print(f"{name}: ok")
    except Exception as exc:
        print(f"{name}: missing ({exc})")
PY

distributed is only required when using --workers for a local Dask cluster.

Bundled Asset

templates/arboreto_grn.py

Preferred Workflow

Confirm the matrix orientation before inference. Arboreto expects observations as rows and genes as columns.
Drop sample-id columns or transpose the matrix before fitting.
Provide a TF whitelist when the user wants biologically narrower networks.
Save the full ranked edge table and a summary JSON.
Treat the output as an inferred regulatory hypothesis set, not a validated causal network.

Quick Start

bash

python3 templates/arboreto_grn.py \
  --input expression.tsv \
  --algorithm grnboost2 \
  --tf-file tf_names.txt \
  --min-importance 0.01 \
  --top-edges 5000 \
  --output grn/network.tsv \
  --summary grn/network.json

If the input is genes-by-samples, transpose it first or use --transpose:

bash

python3 templates/arboreto_grn.py \
  --input expression_genes_by_samples.csv \
  --transpose \
  --algorithm genie3 \
  --workers 4 \
  --output grn/network.tsv \
  --summary grn/network.json

Output Expectations

Good answers should mention:

the exact matrix path and whether it was transposed
which algorithm ran
whether a TF list was used
observation count, gene count, and retained edge count
any distributed or dependency limitation
where the network TSV and summary JSON were written

For h5ad, BAM, CRAM, or mzML dataset triage before GRN inference, activate omics-tools. For statistical modeling on downstream regulon or score tables, activate stat-modeling-tools. For figure generation from network summaries, activate scientific-visualization-tools.

Files

SKILL.md and 1 other file in skills/genomics/grn-tools of DrugClaw/DrugClaw.

SKILL.md
templates/arboreto_grn.py

Open the folder on GitHubat commit 960a6e0

Compare with similar skills

Grn Tools 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.

Grn Tools compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Grn Tools this skillDrugClaw/DrugClaw	126	—	~692	Automated safety check: Pass	Apache-2.0	6 mo ago
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills	3.2k	2 repos	~3k	Automated safety check: Notes	Apache-2.0	today
Ucsc Conservation And Tfbsgoogle-deepmind/science-skills	3.2k	1 repos	~1.9k	Automated safety check: Pass	Apache-2.0	today
ArboretoK-Dense-AI/scientific-agent-skills	48k	1 repos	~2.7k	Automated safety check: Pass	BSD-3-Clause	5 days ago
Bio Chipseq Allele Specific BindingGPTomics/bioSkills	1.2k	2 repos	~3.9k	Automated safety check: Pass	MIT	1 mo ago
Jaspar DatabaseLeonChaoX/qinyan-academic-skills	944	1 repos	~3k	Automated safety check: Pass	CC0-1.0	2 mo ago

Similar skills

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.
3.2k GitHub starsUsed in 2 repos~3k tokens
Research & ScienceAuto-check: notes
Ucsc Conservation And Tfbs
google-deepmind/science-skills
Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser.
3.2k GitHub starsUsed in 1 repo~1.9k tokens
Research & ScienceAuto-check passed
Arboreto
K-Dense-AI/scientific-agent-skills
Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3.
48k GitHub starsUsed in 1 repo~2.7k tokens
Research & ScienceAuto-check passed
Bio Chipseq Allele Specific Binding
GPTomics/bioSkills
Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL +…
1.2k GitHub starsUsed in 2 repos~3.9k tokens
Research & ScienceAuto-check passed
Jaspar Database
LeonChaoX/qinyan-academic-skills
Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs).
944 GitHub starsUsed in 1 repo~3k tokens
Research & ScienceAuto-check passed
Bio Gene Regulatory Networks Grn Inference
GPTomics/bioSkills
Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity…
1.2k GitHub starsUsed in 1 repo~3.5k tokens
Research & ScienceAuto-check passed

Questions about Grn Tools

What does Grn Tools do?

Gene regulatory network workflow guide for transcriptomics and single-cell expression matrices using Arboreto, GRNBoost2, and GENIE3. Grn Tools is an agent skill from DrugClaw/DrugClaw. Gene regulatory network workflow guide for transcriptomics and single-cell expression matrices using Arboreto, GRNBoost2, and GENIE3.

When should I use Grn Tools?

Grn Tools fits situations like: the user asks to infer transcription factor-target links; score regulatory edges; build a GRN from bulk; single-cell expression data.

How do I install Grn Tools in Claude Code?

Run `npx skills add DrugClaw/DrugClaw --skill grn-tools -a claude-code`. Or copy the skill folder (skills/genomics/grn-tools in DrugClaw/DrugClaw) into .claude/skills/grn-tools in your project. Claude Code loads it when a task matches its description.

How do I install Grn Tools in Codex?

Run `npx skills add DrugClaw/DrugClaw --skill grn-tools -a codex`. Or copy the skill folder (skills/genomics/grn-tools in DrugClaw/DrugClaw) into .agents/skills/grn-tools in your project. Codex loads it when a task matches its description.

Can I use Grn Tools 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 DrugClaw/DrugClaw --skill grn-tools -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/grn-tools, .gemini/skills/grn-tools, .github/skills/grn-tools and .opencode/skills/grn-tools in your project.

What does Grn Tools need to run?

Going by SKILL.md and its folder, Grn Tools needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.

Does Grn Tools access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Grn Tools 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 Grn Tools use?

Grn Tools 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.

How many tokens does Grn Tools use?

About 692 tokens (SKILL.md is roughly 2.8k 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 Grn Tools?

Skills that share tags, products or a category with Grn Tools: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), Ucsc Conservation And Tfbs (google-deepmind/science-skills, 3.2k stars), Arboreto (K-Dense-AI/scientific-agent-skills, 48k stars) and Bio Chipseq Allele Specific Binding (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Grn Tools?

DrugClaw (a GitHub organization) maintains it in DrugClaw/DrugClaw, which has 126 GitHub stars. The repository holds 25 skills in this directory. The repository was last updated on March 23, 2026.

Source: DrugClaw/DrugClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Grn Tools

Install Grn Tools

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

GRN Tools

Environment Check

Bundled Asset

Preferred Workflow

Quick Start

Output Expectations

Files

Compare with similar skills

Similar skills

Alphagenome Single Variant Analysis

Ucsc Conservation And Tfbs

Arboreto

Bio Chipseq Allele Specific Binding

Jaspar Database

Bio Gene Regulatory Networks Grn Inference

More from DrugClaw/DrugClaw

Bio DB Tools

Knowledge Graph Tools

Literature Review Tools

Medical Data Tools

Omics Tools

Patent Landscape Tools

Questions about Grn Tools

Install Grn Tools

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

GRN Tools

Environment Check

Bundled Asset

Preferred Workflow

Quick Start

Output Expectations

Related Skills

Files

Compare with similar skills

Similar skills

More from DrugClaw/DrugClaw

Related

Questions about Grn Tools