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Deeptools

Deeptools is an agent skill (a SKILL.md file) from K-Dense-AI/scientific-agent-skills. NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization. It works with Claude Code, Codex, Cursor, Gemini CLI and GitHub Copilot and has 54,643 GitHub stars across a repository of 7 listed skills.

github.com/K-Dense-AI/scientific-agent-skills/skills/deeptools (opens in a new tab)

Data as of from the GitHub API; description from the skill's SKILL.md. Report an error

View on GitHub (opens in a new tab)

Add this skill

Claude

Claude Code loads skills from ~/.claude/skills/ (all projects) or .claude/skills/ (one project):

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/deeptools ~/.claude/skills/deeptools   # personal, or .claude/skills in a project

In the Claude apps, zip the deeptools folder and upload it under Customize > Skills > + > Upload a skill (code execution must be on).

ChatGPT / Codex

Codex reads skills from .agents/skills/ in a repo or ~/.agents/skills/ for every project:

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/deeptools .agents/skills/deeptools   # repo; ~/.agents/skills for all projects

Standalone skills also load in the ChatGPT desktop app.

Cursor

Cursor loads skills from .cursor/skills/ (or ~/.cursor/skills/) and also reads .claude/skills/:

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git
cp -r scientific-agent-skills/skills/deeptools .cursor/skills/deeptools   # project; ~/.cursor/skills for all projects

Source (checked Oct 7, 2026): code.claude.com/docs/en/skills (opens in a new tab), support.claude.com/en/articles/12512180-using-skills-in-claude (opens in a new tab), learn.chatgpt.com/docs/build-skills (opens in a new tab), cursor.com/docs/context/skills (opens in a new tab)

What this skill does

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization. deepTools is a comprehensive suite of Python command-line tools designed for processing and analyzing high-throughput sequencing data. Use deepTools to perform quality control, normalize data, compare samples, and generate publication-quality visualizations for ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, and other NGS experiments.

More skills in K-Dense-AI/scientific-agent-skills

7 skills are listed from this repository.

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FAQ

Deeptools FAQ

Still curious? Email info@appsgit.com.

How do I install the Deeptools skill?

Copy the deeptools folder (the one containing SKILL.md) into ~/.claude/skills/ for Claude Code, .agents/skills/ for Codex or .cursor/skills/ for Cursor. The agent picks it up automatically when a task matches its description.

Is the Deeptools skill free?

Yes. The repository is open source under the MIT license.

Is Deeptools maintained?

The repository's most recent commit was on Oct 19, 2026. Its latest release is v2.72.0. appsgit only lists skills from repositories with a commit in the last six months.