Agent skill

Gi Chromatin

Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.

MITAuto-check: notesResearch & Science

Install Gi Chromatin

skills CLI

$ npx skills add ClawBio/ClawBio --skill gi-chromatin -a claude-code

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

GitHub CLI

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

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 ClawBio/ClawBio --skill gi-chromatin -a codex

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

GitHub CLI

$ gh skill install ClawBio/ClawBio gi-chromatin --agent codex

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

Manual copy

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

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

GitHub CLI

$ gh skill install ClawBio/ClawBio gi-chromatin --agent cursor

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

Manual copy

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

--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 ClawBio/ClawBio --skill gi-chromatin -a gemini-cli

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

GitHub CLI

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

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 ClawBio/ClawBio --skill gi-chromatin -a github-copilot

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

Manual copy

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

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

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/gi-chromatin .opencode/skills/gi-chromatin && 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 "gi-chromatin" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gi-chromatin into .opencode/skills/gi-chromatin/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gi-chromatin", 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: gi-chromatin
GitHub stars: 1.2k
Token cost: ~1.8k tokens
SKILL.md length: 586 words
Files: 6
Skills in repo: 104
Repo updated: Oct 8, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.

Works in 3 steps: Parse: single-record FASTA. → POST to /v1/tasks/chromatin/predict. → Render: report.md (window +…
Tasks that involve Bioinformatics
SKILL.md covers Trigger, Why This Exists, API Backed and Workflow, plus 7 more sections
Runs Python scripts from its folder; calls python; reaches api.genomicintelligence.ai; needs GI_API_KEY

What it does

Gi Chromatin is an agent skill from ClawBio/ClawBio. Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.

Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files (for example `api.py`, `gi_chromatin.py` and `tests/__init__.py`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

Tasks that involve Bioinformatics

Example prompts

“/gi-chromatin”

Requirements

Python 3
A credential in GI_API_KEY

Workflow steps

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

Parse: single-record FASTA.
POST to /v1/tasks/chromatin/predict.
Render: report.md (window + total-annotation counts; per-track detail in result.json).

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. 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:
- python
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:
- api.genomicintelligence.ai
Also links to:
- genomicintelligence.ai
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names these keys or tokens, usually read from environment variables:
- GI_API_KEY
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Gi Chromatin loads about 1.8k tokens when it runs. Until then it costs about 49 tokens; SKILL.md has 586 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~49
When it runs · the whole SKILL.md, loaded when a task matches: ~1.8k

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: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

NoteMentions a .env fileSKILL.md:141
```
cp .env.example .env
```
NoteMentions a .env fileSKILL.md:142
```
set -a && source .env && set +a
```

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 ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 586 words, ~1,803 tokens.

Download SKILL.mdSave it as .claude/skills/gi-chromatin/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.

name: gi-chromatin
description: Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.
license: MIT
metadata.author: ClawBio + Genomic Intelligence
metadata.domain: genomics
metadata.tags: genomics, chromatin, histone, DNase, ATAC, TF-binding, deepsea, dna-lm, gi-api
metadata.version: 0.1.0

🧶 gi-chromatin

You are gi-chromatin, a ClawBio agent that calls the Genomic Intelligence chromatin-annotation model (DeepSEA-style, 919 tracks: histone marks + DNase + TF binding across ENCODE cell types).

⚠️ Remote inference — opt-in required. Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at https://api.genomicintelligence.ai. The same models also run interactively at https://genomicintelligence.ai. Do not submit identifiable patient data without an appropriate data-use agreement. Key setup: see Authentication below.

Trigger

Fire this skill when the user says any of:

"predict chromatin state for this sequence"
"histone mark prediction", "DNase prediction", "ATAC prediction"
"TF binding prediction"
"DeepSEA"
"gi-chromatin", "predict epigenome"
"is this region accessible?"

Do NOT fire when:

The user asks specifically about enhancer activity → gi-enhancer
The user asks for promoter prediction → gi-promoter

Why This Exists

Without it: Running DeepSEA / similar locally needs custom torch envs + weight wrangling.
With it: One CLI call → 919 track predictions per window, in seconds.
Why ClawBio: Hosted G0 DeepSEA inference plus ClawBio reproducibility and chaining.

API Backed

POST https://api.genomicintelligence.ai/v1/tasks/chromatin/predict. Omit model and the API resolves the default — a 919-track DeepSEA-style prediction head. GET /v1/tasks/chromatin/models is the current list.

Contract note. The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task minLength/maxLength on sequence, and a typed, closed options object (an unknown option key is a 422 validation_failed, not a silent ignore). The bounds quoted in this file are the published ones, but the authority is always the served schema: GET https://api.genomicintelligence.ai/v1/openapi.json.

Workflow

Parse: single-record FASTA.
POST to /v1/tasks/chromatin/predict.
Render: report.md (window + total-annotation counts; per-track detail in result.json).

CLI Reference

bash

python skills/gi-chromatin/gi_chromatin.py --demo --output /tmp/gi-chromatin-demo
python skills/gi-chromatin/gi_chromatin.py --input my_region.fa --output report_dir
python clawbio.py run gi-chromatin --demo

Authentication

The skill requires a Genomic Intelligence partner key in GI_API_KEY. Resolution order:

--api-key <value> CLI flag (explicit override).
GI_API_KEY environment variable.
Otherwise: the skill raises a RuntimeError pointing here.

Quick start — ClawBio hackathon key

A shared hackathon-tier key ships in .env.example at the repo root (opt-in only). Caps are per-key and are not published as a fixed number — read RateLimit-Limit / RateLimit-Remaining on any /v1/tasks/ response for the live allowance. The runner keeps them for you: they are in result.json under rate_limit, and a 429 names them on the error line. From wherever the ClawBio files live on your machine:

bash

# Repo root (git clone) — or ~/.claude/plugins/cache/clawbio/clawbio/<version>/ for plugin installs
cp .env.example .env
set -a && source .env && set +a

Show full SKILL.md (217 more words)Show less

Production / heavier use

Request an individual key at contact@genomicintelligence.ai, then:

bash

export GI_API_KEY=gi_yourkeyhere

Demo

bash

python clawbio.py run gi-chromatin --demo

Bundled fixture is an active-promoter region from chr19. Expect dense annotation across active-promoter tracks (H3K4me3, H3K27ac, DNase, etc.) and many called windows.

Gotchas

Big response. 919 tracks × N windows → multi-MB result.json. The report.md summarizes; mine result.json programmatically for specific tracks.
Track labels are in the response. Do not hardcode track indices — read the names from data.tracks.
Length bounds are 200–500,000 bp, published as minLength / maxLength on ChromatinPredictRequest and counted after whitespace is stripped. Both ends are a 422 validation_failed (over-max is not a 413 — 413 is the separate 16 MiB raw-body cap). The skill rejects either locally before spending a request.
200 bp is admission control, not regime. The model's context window is 1,000 bp (bio_spec.context_window_bp on GET /v1/tasks/chromatin/models), so 200–999 bp is accepted and scored — against a window padded out to 1,000 bp. The skill warns when you are under it.
Pre-windowing is unnecessary — the API windows and strides internally.
Hackathon key is shared — GI_API_KEY for heavier use.

Output Structure

output_dir/
├── report.md
├── result.json
└── reproducibility/
    ├── command.sh
    └── environment.json

Integration with Bio Orchestrator

Routes here on: "chromatin", "histone marks", "DNase", "ATAC", "TF binding", "DeepSEA".

Chains with: gi-enhancer (cross-validate enhancer calls against H3K27ac), gi-promoter (active-promoter signature: high H3K4me3 + DNase), variant-annotation (variants in accessible chromatin).

Safety

Research and development use. Not for clinical or diagnostic decisions.

Files

SKILL.md and 5 other files in skills/gi-chromatin of ClawBio/ClawBio.

SKILL.md
api.py
example_data/chromatin_active_promoter_chr19.fa
gi_chromatin.py
tests/__init__.py
tests/test_gi_chromatin.py

Open the folder on GitHubat commit dece754

Compare with similar skills

Gi Chromatin 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.

Gi Chromatin compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Gi Chromatin this skillClawBio/ClawBio	1.2k	—	~1.8k	Automated safety check: Notes	MIT	yesterday
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills	3.2k	2 repos	~3k	Automated safety check: Notes	Apache-2.0	24 days ago
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills	48k	1 repos	~3.2k	Automated safety check: Pass	MIT	4 days ago
Clinvar Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.9k	Automated safety check: Notes	Apache-2.0	24 days ago
Metabolic Study Planneraiming-lab/AutoResearchClaw	15k	—	~1.9k	Automated safety check: Pass	MIT	1 mo ago
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.4k	Automated safety check: Notes	Apache-2.0	24 days ago

Similar skills

Alphagenome Single Variant Analysis
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Research & ScienceAuto-check: notes
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48k GitHub starsUsed in 1 repo~3.2k tokens
Research & ScienceAuto-check passed
Clinvar Database
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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.
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Questions about Gi Chromatin

What does Gi Chromatin do?

Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API. Gi Chromatin is an agent skill from ClawBio/ClawBio. Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.

When should I use Gi Chromatin?

Gi Chromatin fits situations like: tasks that involve Bioinformatics.

How do I install Gi Chromatin in Claude Code?

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

How do I install Gi Chromatin in Codex?

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

Can I use Gi Chromatin 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 ClawBio/ClawBio --skill gi-chromatin -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gi-chromatin, .gemini/skills/gi-chromatin, .github/skills/gi-chromatin and .opencode/skills/gi-chromatin in your project.

What does Gi Chromatin need to run?

Going by SKILL.md and its folder, Gi Chromatin needs Python for the scripts in its folder, the command-line tools its instructions call (python) and credentials named GI_API_KEY. Our summary lists: Python 3; A credential in GI_API_KEY.

Does Gi Chromatin access the network?

SKILL.md names 2 domains. In commands or code: api.genomicintelligence.ai; the agent is likely to contact it when it follows the instructions. As links in the text: genomicintelligence.ai. This is read from the text; nothing was executed.

Is Gi Chromatin safe to install?

Our automated static check of SKILL.md found notes only (mentions a .env file), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Gi Chromatin use?

Gi Chromatin is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Gi Chromatin use?

About 1.8k tokens (SKILL.md is roughly 7.2k 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 Gi Chromatin?

Skills that share tags, products or a category with Gi Chromatin: 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 Gi Chromatin?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 8, 2026.

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

Install Gi Chromatin

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

🧶 gi-chromatin

Trigger

Why This Exists

API Backed

Workflow

CLI Reference

Authentication

Quick start — ClawBio hackathon key

Production / heavier use

Demo

Gotchas

Output Structure

Integration with Bio Orchestrator

Safety

Files

Compare with similar skills

Similar skills

More from ClawBio/ClawBio

Related

Questions about Gi Chromatin