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deepTools NGS Analysis Assistant

Drives the deepTools suite to QC sequencing data, build normalized coverage tracks, and plot heatmaps for ChIP-seq, RNA-seq and ATAC-seq.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Turns Claude into an operator for the deepTools command-line suite used in high-throughput sequencing analysis.

  • Converts BAM alignments into normalized bigWig/bedGraph coverage tracks
  • Runs QC: plotFingerprint, sample correlation, PCA, coverage distribution
  • Builds heatmaps and metaprofiles around TSS or peak regions (computeMatrix → plotHeatmap)
  • Compares treatment vs. control with bamCompare and multi-sample correlation
  • Advises on normalization (RPGC, CPM, RPKM, BPM) with per-organism effective genome sizes
  • Ships a file validation script and a bash workflow generator for ChIP-seq, RNA-seq and ATAC-seq

Who it's for

  • Graduate students and researchers working hands-on with ChIP-seq / ATAC-seq / RNA-seq
  • Anyone who keeps re-looking-up deepTools flags and normalization rules
  • Labs that want reproducible, saved command lines for publication figures
  • Not useful at all if you don't work with genomics data

Examples

  1. "QC my ChIP-seq BAMs" → validates files, generates the chipseq_qc workflow script, runs fingerprint/correlation/PCA and interprets the plots.
  2. "Convert BAM to bigWig for human hg38" → assembles bamCoverage --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --extendReads 200 --ignoreDuplicates.
  3. "Make a TSS heatmap" → walks through computeMatrix reference-point mode then plotHeatmap, suggesting k-means clustering for large region sets.

· · · Install guide · · ·

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 /tmp/sci-skills && mkdir -p ~/.claude/skills && cp -r /tmp/sci-skills/skills/deeptools ~/.claude/skills/

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

  1. Open a terminal.
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills folder: mkdir -p ~/.claude/skills
  4. Copy this skill: cp -r scientific-agent-skills/skills/deeptools ~/.claude/skills/
  5. Install deepTools itself: conda install -c conda-forge -c bioconda deeptools (or uv pip install deepTools==3.5.6)
  6. Verify with bamCoverage --version and samtools --version.
  7. Restart Claude Code and ask something like "Run QC on my ChIP-seq BAM files" to trigger the skill.
View source on GitHub ↗License: MIT