log1p

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
`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"
}

SCMCP

Instructions

Input Schema

Input Schema (JSON Schema)

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