Single Cell Portal Tools#

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

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

Available Tools#

SCP_get_study (Type: SingleCellPortalTool)#

Retrieve one Single Cell Portal study by accession, with its full untruncated description. Access…

SCP_get_study tool specification

Tool Information:

  • Name: SCP_get_study

  • Type: SingleCellPortalTool

  • Description: Retrieve one Single Cell Portal study by accession, with its full untruncated description. Accessions look like ‘SCP1’ and are returned by SCP_search_studies and SCP_list_studies. Private or detached studies are not exposed by the public API and will return an error.

Parameters:

  • accession (string) (required) SCP accession, e.g. ‘SCP1’. Case-insensitive.

Example Usage:

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

SCP_list_studies (Type: SingleCellPortalTool)#

List the public Single Cell Portal study catalog (1000+ studies), sorted by cell count descending…

SCP_list_studies tool specification

Tool Information:

  • Name: SCP_list_studies

  • Type: SingleCellPortalTool

  • Description: List the public Single Cell Portal study catalog (1000+ studies), sorted by cell count descending. Optionally filter by a minimum cell count or a keyword matched against title and description. Use this to find the largest available single-cell studies, or to survey what the portal holds. Returns accession, title, cell count, gene count, and study URL.

Parameters:

  • keyword ([‘string’, ‘null’]) (optional) Optional case-insensitive filter matched against study title and description, e.g. ‘brain’.

  • min_cells ([‘integer’, ‘null’]) (optional) Only return studies with at least this many cells, e.g. 100000.

  • limit ([‘integer’, ‘null’]) (optional) Maximum studies to return (default 20, max 100).

  • description_chars ([‘integer’, ‘null’]) (optional) Truncate each description to this many characters (default 300). Set 0 to omit descriptions.

Example Usage:

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

SCP_search_studies (Type: SingleCellPortalTool)#

Keyword search across the Broad Institute Single Cell Portal, which hosts 1000+ single-cell studi…

SCP_search_studies tool specification

Tool Information:

  • Name: SCP_search_studies

  • Type: SingleCellPortalTool

  • Description: Keyword search across the Broad Institute Single Cell Portal, which hosts 1000+ single-cell studies covering 80M+ cells. Searches study titles, descriptions, and metadata. Returns accession, title, cell count, gene count, and study URL. Example: query=’glioblastoma’. Complements CxGDisc_search_datasets (CELLxGENE) and SCXA_list_experiments (EBI), which index different study sets. Descriptions are truncated; use SCP_get_study for the full text.

Parameters:

  • query (string) (required) Search terms, e.g. ‘lung’, ‘glioblastoma’, ‘COVID-19’, ‘pancreatic islet’. Case-insensitive.

  • limit ([‘integer’, ‘null’]) (optional) Maximum studies to return (default 20, max 100).

  • page ([‘integer’, ‘null’]) (optional) 1-based result page. Use with the total_pages value returned in metadata.

  • description_chars ([‘integer’, ‘null’]) (optional) Truncate each description to this many characters (default 500). Set 0 to omit descriptions.

Example Usage:

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