rank_genes_groups
Identify and rank differentially expressed genes across groups for single-cell RNA sequencing analysis, enabling targeted insights into gene expression patterns and group characterization.
Instructions
Rank genes for characterizing groups, perform differentially expressison analysis
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| corr_method | No | p-value correction method. Used only for 't-test', 't-test_overestim_var', and 'wilcoxon'. | benjamini-hochberg |
| groupby | Yes | The key of the observations grouping to consider. | |
| groups | No | Subset of groups to which comparison shall be restricted, or 'all' for all groups. | all |
| key_added | No | The key in adata.uns information is saved to. | |
| layer | No | Key from adata.layers whose value will be used to perform tests on. | |
| mask_var | No | Select subset of genes to use in statistical tests. | |
| method | No | Method for differential expression analysis. Default is 't-test'. | |
| n_genes | No | The number of genes that appear in the returned tables. Defaults to all genes. | |
| pts | No | Compute the fraction of cells expressing the genes. | |
| rankby_abs | No | Rank genes by the absolute value of the score, not by the score. | |
| reference | No | If 'rest', compare each group to the union of the rest of the group. If a group identifier, compare with respect to this group. | rest |
| tie_correct | No | Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'. | |
| use_raw | No | Use raw attribute of adata if present. |
Input Schema (JSON Schema)
{
"description": "Input schema for the rank_genes_groups tool.",
"properties": {
"corr_method": {
"default": "benjamini-hochberg",
"description": "p-value correction method. Used only for 't-test', 't-test_overestim_var', and 'wilcoxon'.",
"title": "Corr Method",
"type": "string"
},
"groupby": {
"description": "The key of the observations grouping to consider.",
"title": "Groupby",
"type": "string"
},
"groups": {
"anyOf": [
{
"const": "all",
"type": "string"
},
{
"items": {
"type": "string"
},
"type": "array"
}
],
"default": "all",
"description": "Subset of groups to which comparison shall be restricted, or 'all' for all groups.",
"title": "Groups"
},
"key_added": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "The key in adata.uns information is saved to.",
"title": "Key Added"
},
"layer": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Key from adata.layers whose value will be used to perform tests on.",
"title": "Layer"
},
"mask_var": {
"anyOf": [
{
"type": "string"
},
{
"items": {
"type": "boolean"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Select subset of genes to use in statistical tests.",
"title": "Mask Var"
},
"method": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Method for differential expression analysis. Default is 't-test'.",
"title": "Method"
},
"n_genes": {
"anyOf": [
{
"exclusiveMinimum": 0,
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "The number of genes that appear in the returned tables. Defaults to all genes.",
"title": "N Genes"
},
"pts": {
"default": false,
"description": "Compute the fraction of cells expressing the genes.",
"title": "Pts",
"type": "boolean"
},
"rankby_abs": {
"default": false,
"description": "Rank genes by the absolute value of the score, not by the score.",
"title": "Rankby Abs",
"type": "boolean"
},
"reference": {
"default": "rest",
"description": "If 'rest', compare each group to the union of the rest of the group. If a group identifier, compare with respect to this group.",
"title": "Reference",
"type": "string"
},
"tie_correct": {
"default": false,
"description": "Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'.",
"title": "Tie Correct",
"type": "boolean"
},
"use_raw": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Use raw attribute of adata if present.",
"title": "Use Raw"
}
},
"required": [
"groupby"
],
"title": "RankGenesGroupsModel",
"type": "object"
}