Ucsc Cell Browser Tools#

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

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

Available Tools#

UCSCCellBrowser_get_dataset (Type: UCSCCellBrowserTool)#

Get detail for one UCSC Cell Browser dataset by name, including its abstract, organisms, body par…

UCSCCellBrowser_get_dataset tool specification

Tool Information:

  • Name: UCSCCellBrowser_get_dataset

  • Type: UCSCCellBrowserTool

  • Description: Get detail for one UCSC Cell Browser dataset by name, including its abstract, organisms, body parts, diseases, parent collections, and any child datasets. Dataset names look like ‘organoid-22q11’ and come from UCSCCellBrowser_search_datasets. For collection entries, the child_datasets array lists the individual datasets inside.

Parameters:

  • name (string) (required) Dataset identifier, e.g. ‘organoid-22q11’. Returned by UCSCCellBrowser_search_datasets.

Example Usage:

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

UCSCCellBrowser_list_facets (Type: UCSCCellBrowserTool)#

List the distinct values available for a UCSC Cell Browser filter facet, with the number of datas…

UCSCCellBrowser_list_facets tool specification

Tool Information:

  • Name: UCSCCellBrowser_list_facets

  • Type: UCSCCellBrowserTool

  • Description: List the distinct values available for a UCSC Cell Browser filter facet, with the number of datasets carrying each value. Valid facets are ‘organisms’, ‘body_parts’, and ‘diseases’. Call this before UCSCCellBrowser_search_datasets to discover exact filter values, since the catalog uses controlled vocabulary like ‘Human (H. sapiens)’.

Parameters:

  • facet (string) (required) Which facet to enumerate.

Example Usage:

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

UCSCCellBrowser_search_datasets (Type: UCSCCellBrowserTool)#

Search the UCSC Cell Browser catalog of 300+ curated single-cell datasets, filtering by organism,…

UCSCCellBrowser_search_datasets tool specification

Tool Information:

  • Name: UCSCCellBrowser_search_datasets

  • Type: UCSCCellBrowserTool

  • Description: Search the UCSC Cell Browser catalog of 300+ curated single-cell datasets, filtering by organism, body part, disease, or keyword. Each dataset is consistently annotated, so filters are reliable across studies. Example: organism=’Human’, body_part=’brain’. Returns dataset name, label, organisms, body parts, diseases, and browser URL. Use UCSCCellBrowser_list_facets first to see valid filter values.

Parameters:

  • organism ([‘string’, ‘null’]) (optional) Substring match on organism, e.g. ‘Human’, ‘Mouse’, ‘Zebrafish’.

  • body_part ([‘string’, ‘null’]) (optional) Substring match on body part, e.g. ‘brain’, ‘lung’, ‘retina’, ‘blood’.

  • disease ([‘string’, ‘null’]) (optional) Substring match on disease, e.g. ‘cancer’, ‘COVID-19’, ‘Healthy’.

  • keyword ([‘string’, ‘null’]) (optional) Substring match on dataset name or display label, e.g. ‘organoid’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum datasets to return (default 25, max 100).

Example Usage:

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