# tools_reference

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

- Source: https://doutorai.pt/en/components/skills__tools-reference
- Type: Skills
- Category: Scientific
- Downloads: 0
- Site: Doutor AI (https://doutorai.pt/en) - AI tools for small businesses

An open-source community component, curated and adapted by Doutor AI.

## 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)

```bash
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

- 🔒 Full content on the Pro plan (€7.99/month) -
```

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- [PocketBase Deploy](https://doutorai.pt/en/components/skills__pocketbase-deploy): Production deployment for PocketBase. Use when deploying PocketBase to a server, setting up Docker, configuring systemd, reverse proxy (ngin
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- [PocketBase Migrations](https://doutorai.pt/en/components/skills__pocketbase-migrations): Schema migrations and versioning for PocketBase. Use when creating migrations, managing schema versions, syncing collections between environ
- [PocketBase SDK](https://doutorai.pt/en/components/skills__pocketbase-sdk): JavaScript SDK usage for PocketBase client applications. Use when calling PocketBase from frontend or Node.js, authenticating users, subscri

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Content by Doutor AI (https://doutorai.pt/en). When quoting, please cite the source: https://doutorai.pt/en/components/skills__tools-reference