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LogauaEngstrom
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deeptools

Automate deepTools quality control and visualization for NGS sequencing workflows.

18|1|Updated Dec 27, 2025
Search Tags:#visualization#genomics#qc#chip-seq#ngs#deeptools
One-click install
npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill deeptools-logauaengstrom
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: deeptools
Source: https://github.com/LogauaEngstrom/claude-scientific-skills/tree/main/scientific-skills/deeptools
Command: npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill deeptools-logauaengstrom

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

deepTools-based workflows require manual assembling for QC and visualization; this Skill provides ready-made steps for NGS QC and visualization.

Core Features & Use Cases

  • DeepTools-powered QC and visualization across ChIP-seq, RNA-seq, and ATAC-seq workflows.
  • Convert BAM to normalized coverage tracks (bigWig) and generate heatmaps, profiles around genomic features (TSS, peaks), plus correlation and PCA analyses.
  • Easily generate end-to-end workflows from templates and customize per dataset.

Quick Start

Run the provided workflow generator to create a starter script for a chosen deepTools workflow and tailor for your data.

Frequently Asked Questions about deeptools

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate QC metrics and coverage tracks for ChIP-seq and RNA-seq data?▼

Generate publication-quality heatmaps and profiles around TSS or peaks by running deepTools workflow templates that process normalized coverage tracks. This Skill provides ready-made steps to compute and plot genomic signal distributions across features.

What is the best way to automate NGS quality control and visualization workflows?▼

Yes, deepTools supports correlation and PCA analyses for NGS datasets within this Skill's workflows. It leverages deepTools suite scripts to compute and visualize sample similarity, helping you assess data consistency across multiple sequencing libraries.

Do I need pre-aligned BAM files to create bigWig coverage tracks for ATAC-seq?▼

This Skill supports ChIP-seq, RNA-seq, and ATAC-seq workflows for generating quality control metrics and visualizations. It applies deepTools suite scripts to produce coverage tracks, heatmaps, and profiles across these specific NGS applications.

Why does assembling deepTools workflows for NGS visualization require manual effort?▼

You can customize generated deepTools workflows by tailoring the starter script produced by the workflow generator for your chosen dataset. This allows you to adjust parameters for coverage track generation, heatmaps, and profiles as needed.

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