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tools_reference

This document provides a comprehensive reference for all deepTools command-line utilities organized by category.

  • Skills
  • Scientific
  • 4

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

  1. Install the skill (command above).
  2. In Claude Code, describe what you need - the skill turns on by itself when the context fits.
  3. No commands to memorize: you talk in plain language and the skill does the rest.

Install (Claude Code)

mkdir -p .claude/skills/tools-reference && curl -fsSL https://doutorai.pt/data/lib/skills__tools-reference.md -o .claude/skills/tools-reference/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

# deepTools Complete Tool Reference

This document provides a comprehensive reference for all deepTools command-line utilities organized by category.

## BAM and bigWig File Processing Tools

### multiBamSummary

Computes read coverages for genomic regions across multiple BAM files, outputting compressed numpy arrays for downstream correlation and PCA analysis.

**Modes:**
- **bins**: Genome-wide analysis using consecutive equal-sized windows (default 10kb)
- **BED-file**: Restricts analysis to user-specified genomic regions

**Key Parameters:**
- `--bamfiles, -b`: Indexed BAM files (space-sep

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