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Agent skill

Bio Chipseq Super Enhancers

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools.

No licenceAuto-check passedMedia & Creative

Install Bio Chipseq Super Enhancers

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-super-enhancers -a claude-code

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

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-chipseq-super-enhancers --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-chipseq-super-enhancers .claude/skills/bio-chipseq-super-enhancers && 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/

Facts

Skill name
bio-chipseq-super-enhancers
GitHub stars
3.1k
Token cost
~2.1k tokens
SKILL.md length
356 words
Files
4
Skills in repo
279
Repo updated
First seen
Licence
None found

At a glance

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools.

  • Works in 3 steps: BAM file - H3K27ac ChIP-seq aligned reads → Peak file - Called peaks (BED or GFF) → Genome annotation - TSS annotations
  • Studying cell identity genes
  • SKILL.md covers Version Compatibility, Background, ROSE (Rank Ordering of… and Prepare Input Files, plus 7 more sections
  • Runs Python and Shell scripts from its folder; calls python and git; reaches github.com

What it does

Bio Chipseq Super Enhancers is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.

Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `examples/analyze_super_enhancers.py`, `examples/run_rose.sh` and `usage-guide.md`).

It sits in Media & Creative, covering Bioinformatics and Transcription. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.

When your agent uses it

  • Studying cell identity genes
  • Cancer-associated regulatory elements
  • Master transcription factor binding regions that cluster into large enhancer domains

Example prompts

  • “Use the bio-chipseq-super-enhancers skill to identify super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools”
  • “/bio-chipseq-super-enhancers”

Requirements

  • Python 3
  • A Bash shell

Workflow steps

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

  1. BAM file - H3K27ac ChIP-seq aligned reads
  2. Peak file - Called peaks (BED or GFF)
  3. Genome annotation - TSS annotations

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 (Python and Shell), which the agent can run.

    Shell commands in SKILL.md call:

    • python
    • git

    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

Bio Chipseq Super Enhancers loads about 2.1k tokens when it runs. Until then it costs about 70 tokens; SKILL.md has 356 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~70
When it runs · the whole SKILL.md, loaded when a task matches
~2.1k

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 356 words (~2,054 tokens).

“Reference examples tested with: GenomicRanges 1.54+, bedtools 2.31+, ggplot2 3.5+, samtools 1.19+”

— opening of SKILL.md by FreedomIntelligence
name
bio-chipseq-super-enhancers
tool_type
cli
primary_tool
ROSE

Read the full SKILL.md on GitHub

Files

SKILL.md and 3 other files in skills/bio-chipseq-super-enhancers of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/analyze_super_enhancers.py
  • examples/run_rose.sh
  • usage-guide.md

Open the folder on GitHubat commit b1f9b6e

Compare with similar skills

Bio Chipseq Super Enhancers 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.

Bio Chipseq Super Enhancers compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Chipseq Super Enhancers this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k—~2.1kAutomated safety check: PassNone
Bio Chipseq Super EnhancersGPTomics/bioSkills1.2k2 repos~4.1kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
Ucsc Conservation And Tfbsgoogle-deepmind/science-skills3.2k1 repos~1.9kAutomated safety check: PassApache-2.0
ArboretoK-Dense-AI/scientific-agent-skills48k1 repos~2.7kAutomated safety check: PassBSD-3-Clause
Bio Chipseq Allele Specific BindingGPTomics/bioSkills1.2k2 repos~3.9kAutomated safety check: PassMIT

Similar skills

  • Bio Chipseq Super Enhancers

    GPTomics/bioSkills

    Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing.

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  • Ucsc Conservation And Tfbs

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    Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL +…

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  • Jaspar Database

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Categories

Questions about Bio Chipseq Super Enhancers

What does Bio Chipseq Super Enhancers do?

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Bio Chipseq Super Enhancers is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools.

When should I use Bio Chipseq Super Enhancers?

Bio Chipseq Super Enhancers fits situations like: studying cell identity genes; cancer-associated regulatory elements; master transcription factor binding regions that cluster into large enhancer domains.

How do I install Bio Chipseq Super Enhancers in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-super-enhancers -a claude-code`. Or copy the skill folder (skills/bio-chipseq-super-enhancers in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-chipseq-super-enhancers in your project. Claude Code loads it when a task matches its description.

How do I install Bio Chipseq Super Enhancers in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-super-enhancers -a codex`. Or copy the skill folder (skills/bio-chipseq-super-enhancers in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-chipseq-super-enhancers in your project. Codex loads it when a task matches its description.

Can I use Bio Chipseq Super Enhancers 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-chipseq-super-enhancers -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-chipseq-super-enhancers, .gemini/skills/bio-chipseq-super-enhancers, .github/skills/bio-chipseq-super-enhancers and .opencode/skills/bio-chipseq-super-enhancers in your project.

What does Bio Chipseq Super Enhancers need to run?

Going by SKILL.md and its folder, Bio Chipseq Super Enhancers needs Python and a shell for the scripts in its folder and the command-line tools its instructions call (python and git). Our summary lists: Python 3; A Bash shell.

Does Bio Chipseq Super Enhancers 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 Bio Chipseq Super Enhancers 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 Chipseq Super Enhancers use?

No licence was found for Bio Chipseq Super Enhancers or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Chipseq Super Enhancers use?

About 2.1k tokens (SKILL.md is roughly 8.2k 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 Chipseq Super Enhancers?

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

Who maintains Bio Chipseq Super Enhancers?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 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.