mark_var

Identify genes meeting specific conditions (e.g., mitochondrion, ribosomal, hemoglobin) and store results as boolean values in adata.var for quality control metrics calculation.

Instructions

Determine if each gene meets specific conditions and store results in adata.var as boolean values.for example: mitochondrion genes startswith MT-.the tool should be call first when calculate quality control metrics for mitochondrion, ribosomal, harhemoglobin genes. or other qc_vars

Input Schema

Name	Required	Description
`gene_class`	No	Gene class type (Mitochondrion/Ribosomal/Hemoglobin)
`pattern_type`	No	Pattern matching type (startswith/endswith/contains), it should be None when gene_class is not None
`patterns`	No	gene pattern to match, must be a string, it should be None when gene_class is not None
`var_name`	No	Column name that will be added to adata.var, do not set if user does not ask

Input Schema (JSON Schema)

{
  "description": "Determine or mark if each gene meets specific conditions and store results in adata.var as boolean values",
  "properties": {
    "gene_class": {
      "anyOf": [
        {
          "enum": [
            "mitochondrion",
            "ribosomal",
            "hemoglobin"
          ],
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Gene class type (Mitochondrion/Ribosomal/Hemoglobin)",
      "title": "Gene Class"
    },
    "pattern_type": {
      "anyOf": [
        {
          "enum": [
            "startswith",
            "endswith",
            "contains"
          ],
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Pattern matching type (startswith/endswith/contains), it should be None when gene_class is not None",
      "title": "Pattern Type"
    },
    "patterns": {
      "default": null,
      "description": "gene pattern to match, must be a string, it should be None when gene_class is not None",
      "title": "Patterns",
      "type": "string"
    },
    "var_name": {
      "default": null,
      "description": "Column name that will be added to adata.var, do not set if user does not ask",
      "title": "Var Name",
      "type": "string"
    }
  },
  "title": "MarkVarModel",
  "type": "object"
}

SCMCP

mark_var

Instructions

Input Schema

Input Schema (JSON Schema)

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MCP directory API