normalize_total

Normalize per-cell counts to a consistent total, either by median or a specified target sum. Optionally exclude highly expressed genes and apply adjustments to specific layers in single-cell RNA sequencing data.

Instructions

Normalize counts per cell to the same total count

Input Schema

Name	Required	Description
`exclude_highly_expressed`	No	Exclude highly expressed genes for the computation of the normalization factor for each cell.
`inplace`	No	Whether to update adata or return dictionary with normalized copies.
`key_added`	No	Name of the field in adata.obs where the normalization factor is stored.
`layer`	No	Layer to normalize instead of X. If None, X is normalized.
`layer_norm`	No	Specifies how to normalize layers.
`layers`	No	List of layers to normalize. If 'all', normalize all layers.
`max_fraction`	No	If exclude_highly_expressed=True, consider cells as highly expressed that have more counts than max_fraction of the original total counts in at least one cell.
`target_sum`	No	If None, after normalization, each cell has a total count equal to the median of total counts before normalization. If a number is provided, each cell will have this total count after normalization.

Input Schema (JSON Schema)

{
  "description": "Input schema for the normalize_total preprocessing tool.",
  "properties": {
    "exclude_highly_expressed": {
      "default": false,
      "description": "Exclude highly expressed genes for the computation of the normalization factor for each cell.",
      "title": "Exclude Highly Expressed",
      "type": "boolean"
    },
    "inplace": {
      "default": true,
      "description": "Whether to update adata or return dictionary with normalized copies.",
      "title": "Inplace",
      "type": "boolean"
    },
    "key_added": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Name of the field in adata.obs where the normalization factor is stored.",
      "title": "Key Added"
    },
    "layer": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Layer to normalize instead of X. If None, X is normalized.",
      "title": "Layer"
    },
    "layer_norm": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Specifies how to normalize layers.",
      "title": "Layer Norm"
    },
    "layers": {
      "anyOf": [
        {
          "const": "all",
          "type": "string"
        },
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "List of layers to normalize. If 'all', normalize all layers.",
      "title": "Layers"
    },
    "max_fraction": {
      "default": 0.05,
      "description": "If exclude_highly_expressed=True, consider cells as highly expressed that have more counts than max_fraction of the original total counts in at least one cell.",
      "exclusiveMinimum": 0,
      "maximum": 1,
      "title": "Max Fraction",
      "type": "number"
    },
    "target_sum": {
      "anyOf": [
        {
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "If None, after normalization, each cell has a total count equal to the median of total counts before normalization. If a number is provided, each cell will have this total count after normalization.",
      "title": "Target Sum"
    }
  },
  "title": "NormalizeTotalModel",
  "type": "object"
}

SCMCP

normalize_total

Instructions

Input Schema

Input Schema (JSON Schema)

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