# Bio Chipseq Visualization

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker.

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-visualization -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-visualization -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-visualization -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-visualization -g -a gemini-cli -y`

## Description

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Version Compatibility

Reference examples tested with: GenomicRanges 1.54+, deepTools 3.5+

Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- CLI: `<tool> --version` then `<tool> --help` to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.

# ChIP-seq Visualization

**"Create a heatmap of ChIP-seq signal around peaks"** → Generate signal heatmaps, profile plots, and genome browser tracks showing enrichment patterns around genomic features.
- CLI: `deeptools computeMatrix reference-point` → `plotHeatmap`
- R: `Gviz`, `ChIPseeker::plotAvgProf()`

## deepTools - Compute Matrix

**Goal:** Build a signal matrix of ChIP-seq coverage around reference points for downstream heatmaps and profiles.

**Approach:** Use computeMatrix to extract bigWig signal values in windows around genomic features like TSS.

```bash
# Compute signal matrix around TSS
computeMatrix reference-point \
    --referencePoint TSS \
    -b 3000 -a 3000 \              # 3kb upstream and downstream
    -R genes.bed \                  # Reference regions
    -S sample.bw \                  # Signal file (bigWig)
    -o matrix.gz \
    --outFileSortedRegions sorted_genes.bed
```

## deepTools - Scale-Regions

**Goal:** Visualize ChIP signal across gene bodies scaled to a uniform length.

**Approach:** Scale all gene regions to equal size and compute signal with flanking windows.

```bash
# Signal across gene bodies
computeMatrix scale-regions \
    -R genes.bed \
    -S sample1.bw sample2.bw \
    -b 3000 -a 3000 \              # Flanking regions
    -m 5000 \                       # Scaled body length
    -o matrix_scaled.gz
```

## deepTools - Heatmap

**Goal:** Generate a heatmap of ChIP-seq signal intensity across genomic regions.

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-chipseq-visualization/SKILL.md