# Deeptools

NGS analysis toolkit.

- Repository: https://github.com/K-Dense-AI/scientific-agent-skills (55651 stars)
- Category: Engineering
- License: BSD license
- Last updated: 2026-10-26
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -g -a claude-code -y`
Codex: `npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -g -a codex -y`
Cursor: `npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -g -a cursor -y`
Gemini CLI: `npx skills add K-Dense-AI/scientific-agent-skills --skill deeptools -g -a gemini-cli -y`

## Description

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# deepTools: NGS Data Analysis Toolkit

## Overview

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.

**Core capabilities:**
- Convert BAM alignments to normalized coverage tracks (bigWig/bedGraph)
- Quality control assessment (fingerprint, correlation, coverage)
- Sample comparison and correlation analysis
- Heatmap and profile plot generation around genomic features
- Enrichment analysis and peak region visualization

## When to Use This Skill

This skill should be used when:

- **File conversion**: "Convert BAM to bigWig", "generate coverage tracks", "normalize ChIP-seq data"
- **Quality control**: "check ChIP quality", "compare replicates", "assess sequencing depth", "QC analysis"
- **Visualization**: "create heatmap around TSS", "plot ChIP signal", "visualize enrichment", "generate profile plot"
- **Sample comparison**: "compare treatment vs control", "correlate samples", "PCA analysis"
- **Analysis workflows**: "analyze ChIP-seq data", "RNA-seq coverage", "ATAC-seq analysis", "complete workflow"
- **Working with specific file types**: BAM files, bigWig files, BED region files in genomics context

## Quick Start

For users new to deepTools, start with file validation and common workflows:

### 1. Validate Input Files

Before running any analysis, validate BAM, bigWig, and BED files using the validation script:

```bash
python scripts/validate_files.py --bam sample1.bam sample2.bam --bed regions.bed
```

This checks local files, readable BAM/BAI/CSI structure and coordinate order, bigWig headers, and every BED row. It does not establish assembly identity or biological suitability.

### 2. Generate Workflow Template

The rest: https://github.com/K-Dense-AI/scientific-agent-skills/blob/HEAD/skills/deeptools/SKILL.md