clustermarkers
Finds differentially expressed genes (markers) for clusters of T/B cells using Seurat's FindMarkers function. Performs statistical testing between clusters, identifies cluster-defining genes, and automatically runs pathway enrichment analysis (via Enrichr) on significant markers. Generates publication-ready visualizations including volcano plots, dot plots, heatmaps, and enrichment plots.
npx skills add majiayu000/claude-skill-registry --skill clustermarkers-pwwang-immunopipe --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# ClusterMarkers Process Configuration ## Purpose Finds differentially expressed genes (markers) for clusters of T/B cells using Seurat's FindMarkers function. Performs statistical testing between clusters, identifies cluster-defining genes, and automatically runs pathway enrichment analysis (via Enrichr) on significant markers. Generates publication-ready visualizations including volcano plots, dot plots, heatmaps, and enrichment plots. ## When to Use - **After SeuratClustering**: Essential for cluster interpretation and annotation - **Cluster annotation**: Identify marker genes to assign biological meaning to clusters - **Publication preparation**: Generate marker tables, volcano plots, and enrichment figures - **Cell type characterization**: Understand functional differences between cell populations - **Comparative analysis**: Compare clusters to find unique gene expression signatures ## Configuration Structure ### Process Enablement ```toml [ClusterMarkers] cache = true # Cache results for faster re-runs with different visualizations ``` ### Input Specification ```toml [ClusterMarkers.in] srtobj = ["SeuratClustering"] # Seurat object with cluster assignments ``` ### Environment
- Purpose
- When to Use
- Configuration Structure
- Process Enablement
- Input Specification
- Environment Variables
- External References
- Seurat FindMarkers
- Enrichr Databases
- biopipen MarkersFinder
- Configuration Examples
- Minimal Configuration
- Standard Marker Finding (Wilcoxon)
- Publication-Ready MAST Analysis
What does the clustermarkers skill do?
Finds differentially expressed genes (markers) for clusters of T/B cells using Seurat's FindMarkers function. Performs statistical testing between clusters, identifies cluster-defining genes, and automatically runs pathway enrichment analysis (via Enrichr) on significant markers. Generates publication-ready visualizations including volcano plots, dot plots, heatmaps, and enrichment plots.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill clustermarkers-pwwang-immunopipe --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.