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

bio-de-visualization

Maintainer FreedomIntelligence · Last updated April 1, 2026

Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.

OpenClawNanoClawAnalysisWritingbio-de-visualization🧬 bioinformatics (gptomics bio-* suite)bioinformatics — differential expression & transcriptomicsvisualize

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Create visualizations for differential expression analysis using DESeq2 and edgeR built-in plotting functions.
BiocManager::install('EnhancedVolcano').

Source Doc

Excerpt From SKILL.md

Scope

This skill covers DE-specific built-in functions:

DESeq2: plotMA(), plotPCA(), plotDispEsts(), plotCounts()
edgeR: plotMD(), plotBCV(), plotMDS()
Sample distance heatmaps and p-value distributions

For custom ggplot2/matplotlib implementations of volcano, MA, and PCA plots, see data-visualization/specialized-omics-plots.

Installation

install.packages(c('ggplot2', 'pheatmap', 'RColorBrewer', 'ggrepel'))

## MA Plot

**Goal:** Visualize the relationship between mean expression and log fold change to assess DE results.

**Approach:** Plot log fold change against mean normalized counts, highlighting significant genes.

**"Make an MA plot of my DE results"** → Plot mean expression vs. fold change with significant genes colored, using plotMA or ggplot2.

Use cases

Use when visualizing differential expression results.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

deseq2-basics - Generate DESeq2 results for visualization
edger-basics - Generate edgeR results for visualization
de-results - Filter genes before visualization
data-visualization/specialized-omics-plots - Custom ggplot2 volcano/MA/PCA functions
data-visualization/heatmaps-clustering - Advanced heatmap customization