MarkersFinder Process Configuration

Purpose

Flexible marker finding process that wraps Seurat's FindMarkers function for custom group comparisons beyond simple cluster-vs-all analysis. Unlike ClusterMarkers (all-vs-all cluster comparisons), MarkersFinder enables targeted differential expression analysis between specific groups, conditions within cell types, or any custom comparison defined by metadata columns. Automatically performs pathway enrichment analysis on significant markers and generates comprehensive visualizations.

When to Use

• Custom group comparisons: Compare specific clusters (e.g., c1 vs c3)
• Condition effects within cell types: Treatment vs control in T cells
• Targeted differential expression: Focus on biologically meaningful comparisons
• Multi-sample analysis: Find markers across different samples/batches
• Subset-based comparisons: Compare cell states within defined populations
• Complex experimental designs: Multi-condition, multi-factor comparisons

Note: Use ClusterMarkers for standard all-vs-all cluster analysis. Use MarkersFinder for custom comparisons.

Configuration Structure