Data & ReproScientific VisualizationFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-chipseq-visualization

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisWritingbio-chipseq-visualization🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinvisualize

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-visualization

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: deeptools computeMatrix reference-point → plotHeatmap.
R: Gviz, ChIPseeker::plotAvgProf().
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().
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.

Source Doc

Excerpt From SKILL.md

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.


## 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