Skill · em Dados, IA e pesquisa

deeptools

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

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/deeptools
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
nenhum download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

8 arquivos · 82,3 KB · inclui 2 scripts que executam: scripts/validate_files.py, scripts/workflow_generator.py

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/deeptools/.

d=".claude/skills/deeptools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/deeptools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/quick_reference.md" "$u/assets/quick_reference.md" \
  -o "$d/references/effective_genome_sizes.md" "$u/references/effective_genome_sizes.md" \
  -o "$d/references/normalization_methods.md" "$u/references/normalization_methods.md" \
  -o "$d/references/tools_reference.md" "$u/references/tools_reference.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/scripts/validate_files.py" "$u/scripts/validate_files.py" \
  -o "$d/scripts/workflow_generator.py" "$u/scripts/workflow_generator.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/deeptools/.

d="$HOME/.claude/skills/deeptools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/deeptools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/quick_reference.md" "$u/assets/quick_reference.md" \
  -o "$d/references/effective_genome_sizes.md" "$u/references/effective_genome_sizes.md" \
  -o "$d/references/normalization_methods.md" "$u/references/normalization_methods.md" \
  -o "$d/references/tools_reference.md" "$u/references/tools_reference.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/scripts/validate_files.py" "$u/scripts/validate_files.py" \
  -o "$d/scripts/workflow_generator.py" "$u/scripts/workflow_generator.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/deeptools/.

d=".agents/skills/deeptools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/deeptools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/quick_reference.md" "$u/assets/quick_reference.md" \
  -o "$d/references/effective_genome_sizes.md" "$u/references/effective_genome_sizes.md" \
  -o "$d/references/normalization_methods.md" "$u/references/normalization_methods.md" \
  -o "$d/references/tools_reference.md" "$u/references/tools_reference.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/scripts/validate_files.py" "$u/scripts/validate_files.py" \
  -o "$d/scripts/workflow_generator.py" "$u/scripts/workflow_generator.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/deeptools/.

d="$HOME/.agents/skills/deeptools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/deeptools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/quick_reference.md" "$u/assets/quick_reference.md" \
  -o "$d/references/effective_genome_sizes.md" "$u/references/effective_genome_sizes.md" \
  -o "$d/references/normalization_methods.md" "$u/references/normalization_methods.md" \
  -o "$d/references/tools_reference.md" "$u/references/tools_reference.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/scripts/validate_files.py" "$u/scripts/validate_files.py" \
  -o "$d/scripts/workflow_generator.py" "$u/scripts/workflow_generator.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/deeptools/.

d=".agents/skills/deeptools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/deeptools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/quick_reference.md" "$u/assets/quick_reference.md" \
  -o "$d/references/effective_genome_sizes.md" "$u/references/effective_genome_sizes.md" \
  -o "$d/references/normalization_methods.md" "$u/references/normalization_methods.md" \
  -o "$d/references/tools_reference.md" "$u/references/tools_reference.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/scripts/validate_files.py" "$u/scripts/validate_files.py" \
  -o "$d/scripts/workflow_generator.py" "$u/scripts/workflow_generator.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/deeptools/.

d="$HOME/.gemini/antigravity-cli/skills/deeptools"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/deeptools"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/assets/quick_reference.md" "$u/assets/quick_reference.md" \
  -o "$d/references/effective_genome_sizes.md" "$u/references/effective_genome_sizes.md" \
  -o "$d/references/normalization_methods.md" "$u/references/normalization_methods.md" \
  -o "$d/references/tools_reference.md" "$u/references/tools_reference.md" \
  -o "$d/references/workflows.md" "$u/references/workflows.md" \
  -o "$d/scripts/validate_files.py" "$u/scripts/validate_files.py" \
  -o "$d/scripts/workflow_generator.py" "$u/scripts/workflow_generator.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.deeptools

Prévia do SKILL.md

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

# 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 expe…

**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
```
…

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