log1p
Transform single-cell RNA sequencing data by applying the natural logarithm plus one (log(X + 1)) to stabilize variance and normalize expression values for downstream analysis.
Instructions
Logarithmize the data matrix (X = log(X + 1))
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| base | No | Base of the logarithm. Natural logarithm is used by default. | |
| chunk_size | No | Number of observations in the chunks to process the data in. | |
| chunked | No | Process the data matrix in chunks, which will save memory. | |
| layer | No | Entry of layers to transform. | |
| obsm | No | Entry of obsm to transform. |
Input Schema (JSON Schema)
{
"description": "Input schema for the log1p preprocessing tool.",
"properties": {
"base": {
"anyOf": [
{
"type": "integer"
},
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Base of the logarithm. Natural logarithm is used by default.",
"title": "Base"
},
"chunk_size": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of observations in the chunks to process the data in.",
"title": "Chunk Size"
},
"chunked": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Process the data matrix in chunks, which will save memory.",
"title": "Chunked"
},
"layer": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Entry of layers to transform.",
"title": "Layer"
},
"obsm": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Entry of obsm to transform.",
"title": "Obsm"
}
},
"title": "Log1PModel",
"type": "object"
}