---
title: "deepTools - Air Market"
description: "After sequencing reads are aligned, you still need to see whether the data looks right and what the signal does across your regions. This handles that: coverage track conversion, quality checks, and…"
canonical: "https://airmarket.ai/app/deeptools"
---

[Air Market](/) / [Data & Analytics](/category/data) / deepTools

Skill by [K-Dense](/@k-dense-ai)

# deepTools

Turn sequencing alignments into figures you can read

## What this does

After sequencing reads are aligned, you still need to see whether the data looks right and what the signal does across your regions. This handles that: coverage track conversion, quality checks, and heatmaps or profile plots. Reach for it when working with ChIP-seq, RNA-seq or ATAC-seq data.

### Top 3 things it does for you

- Convert BAM files to bigWig coverage tracks
- Check sample quality with correlation and PCA
- Plot signal around transcription start sites

## Information

**deepTools at a glance**

|  |  |
| --- | --- |
| Kind | Skill |
| Publisher | [K-Dense](/@k-dense-ai) |
| Category | [Data & Analytics](/category/data) |
| Works with | Agent Skills - an open standard supported by 40+ agents |
| Version | 1.2 |
| Size | 90 KB |
| Licence | MIT |
| Repository | [k-dense-ai/scientific-agent-skills](https://github.com/k-dense-ai/scientific-agent-skills/tree/81e316bc89f7fda176b092d2bceb959204710b0a/skills/deeptools) |
| GitHub stars | 34,239 (as of Nov 2026) |

## Security report

**Verified.** AIR scanned this exact version of deepTools and flagged nothing. AIR's verdict: **safe**.

**What deepTools's check was run against**

|  |  |
| --- | --- |
| Commit | 81e316bc89f7fda176b092d2bceb959204710b0a |
| Content hash | e0ae9ec38303e05ffaef6161e6289572ce0d2f1508e17289912a8fe916e57ebc |
| Files read | [Browse the files at this exact commit](https://github.com/k-dense-ai/scientific-agent-skills/blob/81e316bc89f7fda176b092d2bceb959204710b0a/skills/deeptools/SKILL.md) |

A scan is named by the exact content it read, not by a version number. A different version is a different artifact, and nothing here applies to a version AIR has not scanned.

[Read the full security report for deepTools](/security/deeptools)

## About deepTools

An NGS analysis toolkit. It converts BAM files to bigWig, runs quality control including correlation, PCA and fingerprints, and produces heatmaps and profiles over features such as transcription start sites and peaks.

It is aimed at ChIP-seq, RNA-seq and ATAC-seq visualization.

## What's inside

- SKILL.md - instructions
- assets/quick_reference.md - reference
- references/core_workflows.md - reference
- references/effective_genome_sizes.md - reference
- references/normalization_methods.md - reference
- references/tools_reference.md - reference
- references/workflows.md - reference
- scripts/validate_files.py - script
- scripts/workflow_generator.py - script

## Questions

### Is deepTools safe to install?

AIR scanned this exact version of deepTools and flagged nothing. AIR's verdict: safe. The verdict is named by the content that was read, at commit 81e316bc89f7, so it cannot drift onto a version nobody scanned. The full report is at https://airmarket.ai/security/deeptools.

### How do I install deepTools?

Open https://airmarket.ai/app/deeptools on Air Market and use the install action: Air Market hands Claude a prompt naming this exact skill, and Claude sets it up. Source, pinned to the exact commit this listing describes: https://github.com/k-dense-ai/scientific-agent-skills/tree/81e316bc89f7fda176b092d2bceb959204710b0a/skills/deeptools. Install from that link, not the branch.

## Related on Air Market

- [More Data & Analytics listings](/category/data)
- [Everything by K-Dense](/@k-dense-ai)

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Canonical URL: <https://airmarket.ai/app/deeptools>