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

[ClusterMarkers]
cache = true  # Cache results for faster re-runs with different visualizations