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deeptools

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

by K-Dense-AI 40k MIT Updated Aug 31, 2026
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deeptools skill by K-Dense-AI
deeptools — Data skill by K-Dense-AI

Overview

deeptools is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.”. The project has 40k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/deeptools`.

What deeptools does

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.

What’s inside

The SKILL.md for deeptools is organised into these sections:

  • Overview
  • When to Use This Skill
  • Quick Start
  • 1. Validate Input Files
  • 2. Generate Workflow Template
  • 3. Most Common Operations
  • Installation
  • Core Workflows and Tool Categories
  • Normalization Methods
  • Effective Genome Sizes
  • Common Parameters Across Tools
  • Best Practices

Installation

Add deeptools to your agent with:

git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/deeptools

Review a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.

Supported agents

Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.

License

deeptools is published under the MIT license.

Strengths

  • Clear MIT license — safe to read and adapt within its terms
  • Ships in K-Dense-AI/scientific-agent-skills, an established project with 40,410 GitHub stars
  • Actively maintained — repository updated in the last 30 days
  • Its repository gained 6,589 GitHub stars over the last 13 days

Author

K-Dense-AI 42 skills in the catalog · GitHub profile ↗
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Topics

agent-skillsai-scientistbioinformaticschemoinformaticsclaudeclaude-skillsclaudecodeclinical-researchcomputational-biologydata-analysisdrug-discoverygenomicsmaterials-sciencemetabolomicsproteomicsscientific-computingscientific-visualization
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Frequently asked questions

What does deeptools do?
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
How do I install deeptools?
Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/deeptools in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
Is deeptools free to use?
Yes. deeptools is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
Where does deeptools come from?
deeptools ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 40,410 GitHub stars apply to that whole collection, not to this skill on its own.

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