Cortexa research tool·genomics·cellxgene_census

CELLxGENE Get Expression Data

Query gene expression data from CELLxGENE Census (50M+ cells, 60K+ genes). CRITICAL: At least one filter REQUIRED - unfiltered queries timeout. Start with: obs_value_filter='tissue_general == "lung" and disease == "normal"' AND var_value_filter='feature_name in ["TP53", "EGFR"]'. Returns AnnData summary (dimensions, metadata). For full matrix data, use Python API with sufficient memory.

Livelast probed 2026-04-30 23:07Z· 112msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 112ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "census_version": {
      "default": "stable",
      "description": "Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.",
      "type": "string"
    },
    "obs_column_names": {
      "description": "Cell metadata columns to include",
      "items": {
        "type": "string"
      },
      "type": "array"
    },
    "obs_value_filter": {
      "description": "REQUIRED (or use var_value_filter) - Cell filter. Common values: tissue_general (brain, lung, heart, blood, liver), cell_type (T cell, B cell, neuron, macrophage), disease (normal, COVID-19, Alzheimer disease). Example: 'tissue_general == \"lung\" and disease == \"normal\"'",
      "type": "string"
    },
    "operation": {
      "default": "get_anndata",
      "description": "Operation type",
      "enum": [
        "get_anndata"
      ],
      "type": "string"
    },
    "organism": {
      "default": "Homo sapiens",
      "description": "Organism name",
      "enum": [
        "Homo sapiens",
        "Mus musculus"
      ],
      "type": "string"
    },
    "var_column_names": {
      "description": "Gene metadata columns to include",
      "items": {
        "type": "string"
      },
      "type": "array"
    },
    "var_value_filter": {
      "description": "REQUIRED (or use obs_value_filter) - Gene filter by symbol or Ensembl ID. Examples: 'feature_name in [\"TP53\", \"BRCA1\", \"EGFR\"]', 'feature_name == \"CD4\"'. Common genes: TP53, EGFR, BRCA1, CD4, CD8A, IL6, TNF, GAPDH.",
      "type": "string"
    }
  },
  "required": [
    "operation"
  ],
  "type": "object"
}

Examples (1)

Default CELLxGENE Get Expression Data call

public-safeinput

{
  "obs_column_names": [],
  "operation": "",
  "var_column_names": []
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_CELLxGENE_get_expression_data
Tool name: CELLxGENE_get_expression_data
Added: 2026-04-30 22:47Z
Tags: tooluniverse

CELLxGENE Get Expression Data

Livelast probed 2026-04-30 23:07Z· 112msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "census_version": { "default": "stable", "description": "Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.", "type": "string" }, "obs_column_names": { "description": "Cell metadata columns to include", "items": { "type": "string" }, "type": "array" }, "obs_value_filter": { "description": "REQUIRED (or use var_value_filter) - Cell filter. Common values: tissue_general (brain, lung, heart, blood, liver), cell_type (T cell, B cell, neuron, macrophage), disease (normal, COVID-19, Alzheimer disease). Example: 'tissue_general == \"lung\" and disease == \"normal\"'", "type": "string" }, "operation": { "default": "get_anndata", "description": "Operation type", "enum": [ "get_anndata" ], "type": "string" }, "organism": { "default": "Homo sapiens", "description": "Organism name", "enum": [ "Homo sapiens", "Mus musculus" ], "type": "string" }, "var_column_names": { "description": "Gene metadata columns to include", "items": { "type": "string" }, "type": "array" }, "var_value_filter": { "description": "REQUIRED (or use obs_value_filter) - Gene filter by symbol or Ensembl ID. Examples: 'feature_name in [\"TP53\", \"BRCA1\", \"EGFR\"]', 'feature_name == \"CD4\"'. Common genes: TP53, EGFR, BRCA1, CD4, CD8A, IL6, TNF, GAPDH.", "type": "string" } }, "required": [ "operation" ], "type": "object" }