scale

scale

Normalize single-cell RNA sequencing data by scaling to unit variance and zero mean. Adjust parameters like zero-centering, clipping, and layer selection for efficient preprocessing.

Instructions

Scale data to unit variance and zero mean

Input Schema

Name	Required	Description
`layer`	No	If provided, which element of layers to scale.
`mask_obs`	No	Boolean mask or string referring to obs column for subsetting observations.
`max_value`	No	Clip (truncate) to this value after scaling. If None, do not clip.
`obsm`	No	If provided, which element of obsm to scale.
`zero_center`	No	If False, omit zero-centering variables to handle sparse input efficiently.

Input Schema (JSON Schema)

{
  "description": "Input schema for the scale preprocessing tool.",
  "properties": {
    "layer": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "If provided, which element of layers to scale.",
      "title": "Layer"
    },
    "mask_obs": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "boolean"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Boolean mask or string referring to obs column for subsetting observations.",
      "title": "Mask Obs"
    },
    "max_value": {
      "anyOf": [
        {
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Clip (truncate) to this value after scaling. If None, do not clip.",
      "title": "Max Value"
    },
    "obsm": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "If provided, which element of obsm to scale.",
      "title": "Obsm"
    },
    "zero_center": {
      "default": true,
      "description": "If False, omit zero-centering variables to handle sparse input efficiently.",
      "title": "Zero Center",
      "type": "boolean"
    }
  },
  "title": "ScaleModel",
  "type": "object"
}

SCMCP

Instructions

Input Schema

Input Schema (JSON Schema)

Other Tools from SCMCP

Related Tools

MCP directory API