Cellxgene Discovery Tools#

Configuration File: cellxgene_discovery_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the cellxgene_discovery_tools.json configuration file.

Available Tools#

CxGDisc_get_collection (Type: CellxGeneDiscoveryTool)#

Get detailed information about a specific CellxGene Discovery collection, including all datasets …

CxGDisc_get_collection tool specification

Tool Information:

  • Name: CxGDisc_get_collection

  • Type: CellxGeneDiscoveryTool

  • Description: Get detailed information about a specific CellxGene Discovery collection, including all datasets and every tissue, disease, organism, cell-type, and assay label (cell-type lists are not truncated). Example: collection ‘48259aa8-f168-4bf5-b797-af8e88da6637’ is the Human Breast Cell Atlas with 5 datasets totaling 2.8M cells; its integrated dataset currently exposes 26 cell types.

Parameters:

  • collection_id (string) (required) Collection UUID from CellxGene Discovery (e.g., ‘48259aa8-f168-4bf5-b797-af8e88da6637’ for Human Breast Cell Atlas).

Example Usage:

query = {
    "name": "CxGDisc_get_collection",
    "arguments": {
        "collection_id": "example_value"
    }
}
result = tu.run(query)

CxGDisc_list_collections (Type: CellxGeneDiscoveryTool)#

List curated single-cell RNA-seq collections from CZI CellxGene Discovery. Each collection is a p…

CxGDisc_list_collections tool specification

Tool Information:

  • Name: CxGDisc_list_collections

  • Type: CellxGeneDiscoveryTool

  • Description: List curated single-cell RNA-seq collections from CZI CellxGene Discovery. Each collection is a published dataset group with DOI, typically corresponding to a paper. Returns the complete (untruncated) collection description, collection name, DOI, dataset count, total cell count, curator info, exact total/returned counts, and explicit pagination fields. Follow next_offset while has_more is true to retrieve later collections.

Parameters:

  • limit (integer) (optional) Maximum number of collections to return (1-100). Default: 20.

  • offset (integer) (optional) Zero-based result offset. Default: 0. Use the returned next_offset to retrieve the next slice.

Example Usage:

query = {
    "name": "CxGDisc_list_collections",
    "arguments": {
    }
}
result = tu.run(query)

CxGDisc_search_datasets (Type: CellxGeneDiscoveryTool)#

Search CellxGene Discovery single-cell RNA-seq datasets by tissue, disease, organism, or cell typ…

CxGDisc_search_datasets tool specification

Tool Information:

  • Name: CxGDisc_search_datasets

  • Type: CellxGeneDiscoveryTool

  • Description: Search CellxGene Discovery single-cell RNA-seq datasets by tissue, disease, organism, or cell type. Results are sorted by cell count (largest first) and include exact total/returned counts plus explicit pagination fields. Follow next_offset while has_more is true to retrieve later matching datasets.

Parameters:

  • tissue (string) (optional) Filter by tissue name (e.g., ‘lung’, ‘brain’, ‘heart’, ‘kidney’, ‘liver’). Case-insensitive partial match.

  • disease (string) (optional) Filter by disease (e.g., ‘cancer’, ‘COVID’, ‘Alzheimer’, ‘normal’). Case-insensitive partial match.

  • organism (string) (optional) Filter by organism (e.g., ‘Homo sapiens’, ‘Mus musculus’). Case-insensitive partial match.

  • cell_type (string) (optional) Filter by cell type (e.g., ‘T cell’, ‘neuron’, ‘macrophage’, ‘epithelial’). Case-insensitive partial match.

  • limit (integer) (optional) Maximum datasets to return (1-100). Default: 20.

  • offset (integer) (optional) Zero-based result offset. Default: 0. Use the returned next_offset to retrieve the next slice.

Example Usage:

query = {
    "name": "CxGDisc_search_datasets",
    "arguments": {
    }
}
result = tu.run(query)