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deepTools NGS Analysis Assistant

Guides Claude through deepTools workflows for converting, QC-ing and visualizing ChIP-seq, RNA-seq and ATAC-seq data.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

  • Builds bamCoverage/bamCompare commands to turn BAM alignments into normalized bigWig or bedGraph coverage tracks.
  • Walks through quality control: correlation, PCA, fingerprint and coverage checks.
  • Composes heatmaps and profile plots around TSS or peak regions via computeMatrix → plotHeatmap/plotProfile.
  • Recommends the right normalization (RPGC, CPM, RPKM, BPM) and supplies effective genome sizes per assembly.
  • Ships helper scripts: validate_files.py for input checks and workflow_generator.py for ready-to-run pipeline templates.

Who it's for

  • Bioinformaticians and grad students working with ChIP-seq, ATAC-seq or RNA-seq data.
  • Researchers tired of digging through deepTools docs for the right flags.
  • Anyone who wants reproducible, documented NGS analysis scripts fast.

Examples

  1. "Convert my ChIP-seq BAM to an RPGC-normalized bigWig for hg38" → bamCoverage command with extendReads, ignoreDuplicates and the correct effective genome size.
  2. "Check replicate correlation and ChIP enrichment" → generated QC script chaining multiBamSummary, plotCorrelation and plotFingerprint.
  3. "Make a heatmap of signal around gene TSS" → computeMatrix in reference-point mode followed by plotHeatmap with clustering options.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/deeptools/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/deeptools folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/deeptools/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/deeptools ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and move to the folder where you keep source code.
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Copy the skill into Claude's skills folder: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/deeptools ~/.claude/skills/
  4. Install deepTools: uv pip install deepTools==3.5.6, or preferably conda install -c conda-forge -c bioconda deeptools.
  5. Also install samtools for BAM indexing: conda install -c bioconda samtools.
  6. Restart Claude Code and try a prompt like "Convert this BAM to a normalized bigWig" to trigger the skill.
View source on GitHub ↗License: MIT