# Deeptools (agent skill)

> 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 47,813 GitHub stars across a repository of 7 listed skills.

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.

## Key facts

| Fact | Value |
|---|---|
| Repository | https://github.com/K-Dense-AI/scientific-agent-skills |
| Skill path | skills/deeptools/SKILL.md |
| Skill name | deeptools |
| GitHub stars | 47,813 |
| Installs on skills.sh | not listed |
| License | MIT |
| Skills in repo | 7 |
| Plugin marketplace | no |
| Official | no |
| Works with | Claude Code, Codex, Cursor, Gemini CLI, GitHub Copilot |
| Category | Data & analysis |
| Last commit | Oct 5, 2026 |

## Add this skill

### Claude Code

```sh
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 skill folder and upload it under Customize > Skills > + > Upload a skill (code execution must be on).

### ChatGPT / Codex

```sh
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
```

### Cursor

```sh
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
```

Sources (checked 2026-10-07): https://code.claude.com/docs/en/skills, https://support.claude.com/en/articles/12512180-using-skills-in-claude, https://learn.chatgpt.com/docs/build-skills, https://cursor.com/docs/context/skills

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Canonical page: https://appsgit.com/skills/k-dense-ai-deeptools
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