highly_variable_genes

Identify and annotate highly variable genes from single-cell RNA sequencing data, enabling focused analysis on key genes using configurable dispersion and expression cutoffs.

Instructions

Annotate highly variable genes

Input Schema

Name	Required	Description	Default
`batch_key`	No	Key in adata.obs for batch information.
`check_values`	No	Check if counts are integers for seurat_v3 flavor.
`flavor`	No	Method for identifying highly variable genes.	seurat
`layer`	No	If provided, use adata.layers[layer] for expression values.
`max_disp`	No	Maximum dispersion cutoff for gene selection.
`max_mean`	No	Maximum mean expression cutoff for gene selection.
`min_disp`	No	Minimum dispersion cutoff for gene selection.
`min_mean`	No	Minimum mean expression cutoff for gene selection.
`n_bins`	No	Number of bins for mean expression binning.
`n_top_genes`	No	Number of highly-variable genes to keep. Mandatory if `flavor='seurat_v3'
`span`	No	Fraction of data used for loess model fit in seurat_v3.
`subset`	No	Inplace subset to highly-variable genes if True.

Input Schema (JSON Schema)

{
  "description": "Input schema for the highly_variable_genes preprocessing tool.",
  "properties": {
    "batch_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Key in adata.obs for batch information.",
      "title": "Batch Key"
    },
    "check_values": {
      "default": true,
      "description": "Check if counts are integers for seurat_v3 flavor.",
      "title": "Check Values",
      "type": "boolean"
    },
    "flavor": {
      "default": "seurat",
      "description": "Method for identifying highly variable genes.",
      "enum": [
        "seurat",
        "cell_ranger",
        "seurat_v3",
        "seurat_v3_paper"
      ],
      "title": "Flavor",
      "type": "string"
    },
    "layer": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "If provided, use adata.layers[layer] for expression values.",
      "title": "Layer"
    },
    "max_disp": {
      "default": null,
      "description": "Maximum dispersion cutoff for gene selection.",
      "title": "Max Disp",
      "type": "number"
    },
    "max_mean": {
      "default": 3,
      "description": "Maximum mean expression cutoff for gene selection.",
      "title": "Max Mean",
      "type": "number"
    },
    "min_disp": {
      "default": 0.5,
      "description": "Minimum dispersion cutoff for gene selection.",
      "title": "Min Disp",
      "type": "number"
    },
    "min_mean": {
      "default": 0.0125,
      "description": "Minimum mean expression cutoff for gene selection.",
      "title": "Min Mean",
      "type": "number"
    },
    "n_bins": {
      "default": 20,
      "description": "Number of bins for mean expression binning.",
      "exclusiveMinimum": 0,
      "title": "N Bins",
      "type": "integer"
    },
    "n_top_genes": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Number of highly-variable genes to keep. Mandatory if `flavor='seurat_v3'",
      "title": "N Top Genes"
    },
    "span": {
      "default": 0.3,
      "description": "Fraction of data used for loess model fit in seurat_v3.",
      "exclusiveMaximum": 1,
      "exclusiveMinimum": 0,
      "title": "Span",
      "type": "number"
    },
    "subset": {
      "default": false,
      "description": "Inplace subset to highly-variable genes if True.",
      "title": "Subset",
      "type": "boolean"
    }
  },
  "title": "HighlyVariableGenesModel",
  "type": "object"
}

SCMCP

highly_variable_genes

Instructions

Input Schema

Input Schema (JSON Schema)

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MCP directory API