rank_genes_groups

Identify and rank differentially expressed genes across groups for single-cell RNA sequencing analysis, enabling targeted insights into gene expression patterns and group characterization.

Instructions

Rank genes for characterizing groups, perform differentially expressison analysis

Input Schema

Name	Required	Description	Default
`corr_method`	No	p-value correction method. Used only for 't-test', 't-test_overestim_var', and 'wilcoxon'.	benjamini-hochberg
`groupby`	Yes	The key of the observations grouping to consider.
`groups`	No	Subset of groups to which comparison shall be restricted, or 'all' for all groups.	all
`key_added`	No	The key in adata.uns information is saved to.
`layer`	No	Key from adata.layers whose value will be used to perform tests on.
`mask_var`	No	Select subset of genes to use in statistical tests.
`method`	No	Method for differential expression analysis. Default is 't-test'.
`n_genes`	No	The number of genes that appear in the returned tables. Defaults to all genes.
`pts`	No	Compute the fraction of cells expressing the genes.
`rankby_abs`	No	Rank genes by the absolute value of the score, not by the score.
`reference`	No	If 'rest', compare each group to the union of the rest of the group. If a group identifier, compare with respect to this group.	rest
`tie_correct`	No	Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'.
`use_raw`	No	Use raw attribute of adata if present.

Input Schema (JSON Schema)

{
  "description": "Input schema for the rank_genes_groups tool.",
  "properties": {
    "corr_method": {
      "default": "benjamini-hochberg",
      "description": "p-value correction method. Used only for 't-test', 't-test_overestim_var', and 'wilcoxon'.",
      "title": "Corr Method",
      "type": "string"
    },
    "groupby": {
      "description": "The key of the observations grouping to consider.",
      "title": "Groupby",
      "type": "string"
    },
    "groups": {
      "anyOf": [
        {
          "const": "all",
          "type": "string"
        },
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        }
      ],
      "default": "all",
      "description": "Subset of groups to which comparison shall be restricted, or 'all' for all groups.",
      "title": "Groups"
    },
    "key_added": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The key in adata.uns information is saved to.",
      "title": "Key Added"
    },
    "layer": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Key from adata.layers whose value will be used to perform tests on.",
      "title": "Layer"
    },
    "mask_var": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "items": {
            "type": "boolean"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Select subset of genes to use in statistical tests.",
      "title": "Mask Var"
    },
    "method": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Method for differential expression analysis. Default is 't-test'.",
      "title": "Method"
    },
    "n_genes": {
      "anyOf": [
        {
          "exclusiveMinimum": 0,
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "The number of genes that appear in the returned tables. Defaults to all genes.",
      "title": "N Genes"
    },
    "pts": {
      "default": false,
      "description": "Compute the fraction of cells expressing the genes.",
      "title": "Pts",
      "type": "boolean"
    },
    "rankby_abs": {
      "default": false,
      "description": "Rank genes by the absolute value of the score, not by the score.",
      "title": "Rankby Abs",
      "type": "boolean"
    },
    "reference": {
      "default": "rest",
      "description": "If 'rest', compare each group to the union of the rest of the group. If a group identifier, compare with respect to this group.",
      "title": "Reference",
      "type": "string"
    },
    "tie_correct": {
      "default": false,
      "description": "Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'.",
      "title": "Tie Correct",
      "type": "boolean"
    },
    "use_raw": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Use raw attribute of adata if present.",
      "title": "Use Raw"
    }
  },
  "required": [
    "groupby"
  ],
  "title": "RankGenesGroupsModel",
  "type": "object"
}

SCMCP

rank_genes_groups

Instructions

Input Schema

Input Schema (JSON Schema)

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