score_genes
Analyze gene expression data by scoring a set of genes based on their average expression levels, using configurable parameters like reference gene sampling and expression bins for accurate results.
Instructions
Score a set of genes based on their average expression
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| ctrl_size | No | Number of reference genes to be sampled from each bin. | |
| gene_pool | No | Genes for sampling the reference set. Default is all genes. | |
| n_bins | No | Number of expression level bins for sampling. | |
| random_state | No | The random seed for sampling. | |
| score_name | No | Name of the field to be added in .obs. | score |
| use_raw | No | Whether to use raw attribute of adata. Defaults to True if .raw is present. |
Input Schema (JSON Schema)
{
"description": "Input schema for the score_genes tool that calculates gene scores based on average expression.",
"properties": {
"ctrl_size": {
"default": 50,
"description": "Number of reference genes to be sampled from each bin.",
"exclusiveMinimum": 0,
"title": "Ctrl Size",
"type": "integer"
},
"gene_pool": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Genes for sampling the reference set. Default is all genes.",
"title": "Gene Pool"
},
"n_bins": {
"default": 25,
"description": "Number of expression level bins for sampling.",
"exclusiveMinimum": 0,
"title": "N Bins",
"type": "integer"
},
"random_state": {
"default": 0,
"description": "The random seed for sampling.",
"title": "Random State",
"type": "integer"
},
"score_name": {
"default": "score",
"description": "Name of the field to be added in .obs.",
"title": "Score Name",
"type": "string"
},
"use_raw": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether to use raw attribute of adata. Defaults to True if .raw is present.",
"title": "Use Raw"
}
},
"title": "ScoreGenesModel",
"type": "object"
}