combat
Correct batch effects in single-cell RNA sequencing data using a categorical annotation key and optional covariates, enabling accurate downstream analysis without manual coding.
Instructions
ComBat function for batch effect correction
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| covariates | No | Additional covariates besides the batch variable such as adjustment variables or biological condition. | |
| key | No | Key to a categorical annotation from adata.obs that will be used for batch effect removal. | batch |
Input Schema (JSON Schema)
{
"description": "Input schema for the combat batch effect correction tool.",
"properties": {
"covariates": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Additional covariates besides the batch variable such as adjustment variables or biological condition.",
"title": "Covariates"
},
"key": {
"default": "batch",
"description": "Key to a categorical annotation from adata.obs that will be used for batch effect removal.",
"title": "Key",
"type": "string"
}
},
"title": "CombatModel",
"type": "object"
}