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
| 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. |
Input Schema (JSON Schema)
{
"description": "Input schema for the marker gene overlap tool.",
"properties": {
"adj_pval_threshold": {
"anyOf": [
{
"exclusiveMinimum": 0,
"maximum": 1,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "A significance threshold on the adjusted p-values to select marker genes.",
"title": "Adj Pval Threshold"
},
"key": {
"default": "rank_genes_groups",
"description": "The key in adata.uns where the rank_genes_groups output is stored.",
"title": "Key",
"type": "string"
},
"key_added": {
"default": "marker_gene_overlap",
"description": "Name of the .uns field that will contain the marker overlap scores.",
"title": "Key Added",
"type": "string"
},
"method": {
"default": "overlap_count",
"description": "Method to calculate marker gene overlap: 'overlap_count', 'overlap_coef', or 'jaccard'.",
"title": "Method",
"type": "string"
},
"normalize": {
"anyOf": [
{
"enum": [
"reference",
"data"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Normalization option for the marker gene overlap output. Only applicable when method is 'overlap_count'.",
"title": "Normalize"
},
"top_n_markers": {
"anyOf": [
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "The number of top data-derived marker genes to use. By default the top 100 marker genes are used.",
"title": "Top N Markers"
}
},
"title": "MarkerGeneOverlapModel",
"type": "object"
}