marker_gene_overlap
Identify and compare overlapping marker genes between experimental data and reference sets using methods like overlap count, coefficient, or Jaccard index. Supports customization via normalization, adjusted p-value thresholds, and top N selection.
Instructions
Calculate overlap between data-derived marker genes and reference markers
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| adj_pval_threshold | No | A significance threshold on the adjusted p-values to select marker genes. | |
| key | No | The key in adata.uns where the rank_genes_groups output is stored. | rank_genes_groups |
| key_added | No | Name of the .uns field that will contain the marker overlap scores. | marker_gene_overlap |
| method | No | Method to calculate marker gene overlap: 'overlap_count', 'overlap_coef', or 'jaccard'. | overlap_count |
| normalize | No | Normalization option for the marker gene overlap output. Only applicable when method is 'overlap_count'. | |
| top_n_markers | No | The number of top data-derived marker genes to use. By default the top 100 marker genes are used. |