Cellmarker Tools#

Configuration File: cellmarker_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

CellMarker_list_cell_types (Type: CellMarkerTool)#

List available cell types in the CellMarker 2.0 database for a given tissue and species. Returns …

CellMarker_list_cell_types tool specification

Tool Information:

  • Name: CellMarker_list_cell_types

  • Type: CellMarkerTool

  • Description: List available cell types in the CellMarker 2.0 database for a given tissue and species. Returns all annotated cell types found in that tissue context. Use this to explore what cell types have been characterized in a specific tissue, or to get an overview of CellMarker’s coverage. Supports both normal and cancer cell contexts.

Parameters:

  • tissue_type (string) (optional) Tissue type to list cell types for (e.g., ‘Blood’, ‘Lung’, ‘Brain’, ‘Liver’). If omitted, returns a global list.

  • species (string) (optional) Species to query (default: ‘Human’)

  • cell_class (string) (optional) Cell class filter: ‘all’ for normal+cancer (default), ‘cancer’ for cancer cells only

Example Usage:

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

CellMarker_search_by_cell_type (Type: CellMarkerTool)#

Search the CellMarker 2.0 database for marker genes of a cell-type phrase. Matching respects phra…

CellMarker_search_by_cell_type tool specification

Tool Information:

  • Name: CellMarker_search_by_cell_type

  • Type: CellMarkerTool

  • Description: Search the CellMarker 2.0 database for marker genes of a cell-type phrase. Matching respects phrase boundaries, so ‘T cell’ includes qualified T-cell names but does not incorrectly match ‘Fat cell’ or ‘Mast cell’. Marker summaries and curated records use limit/offset pagination with separate totals and has_more flags. Example: ‘T cell’ returns CD3D, CD3E, and CD3G; ‘Macrophage’ returns CD68 and CD163.

Parameters:

  • cell_name (string) (required) Cell type name to search for (e.g., ‘T cell’, ‘Macrophage’, ‘B cell’, ‘Fibroblast’)

  • species (string) (optional) Species filter. If omitted, searches both species.

  • tissue_type (string) (optional) Filter results by tissue type (e.g., ‘Blood’, ‘Lung’, ‘Brain’). Case-insensitive partial match.

  • limit ([‘integer’, ‘null’]) (optional) Maximum records to return. Default 200; total_records reports how many matched, so raise this or page with offset when it is larger.

  • offset ([‘integer’, ‘null’]) (optional) Records to skip before returning, for paging through total_records. Use data.next_offset for the next page.

Example Usage:

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

CellMarker_search_by_gene (Type: CellMarkerTool)#

Search the CellMarker 2.0 database for cell types that express a given marker gene. Returns curat…

CellMarker_search_by_gene tool specification

Tool Information:

  • Name: CellMarker_search_by_gene

  • Type: CellMarkerTool

  • Description: Search the CellMarker 2.0 database for cell types that express a given marker gene. Returns curated record-level annotations with limit/offset pagination and explicit total/has_more metadata. CellMarker 2.0 covers human and mouse cell types across many tissues. Example: CD3D marks T cells, CD68 marks macrophages, and EPCAM marks epithelial cells.

Parameters:

  • gene_symbol (string) (required) Gene symbol to search for (e.g., ‘CD3D’, ‘CD68’, ‘EPCAM’, ‘MS4A1’)

  • species (string) (optional) Species filter: ‘Human’ or ‘Mouse’. If omitted, searches both species.

  • tissue_type (string) (optional) Filter results by tissue type (e.g., ‘Blood’, ‘Lung’, ‘Brain’). Case-insensitive partial match.

  • limit ([‘integer’, ‘null’]) (optional) Maximum records to return. Default 200; total_records reports how many matched, so raise this or page with offset when it is larger.

  • offset ([‘integer’, ‘null’]) (optional) Records to skip before returning, for paging through total_records. Use data.next_offset for the next page.

Example Usage:

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

CellMarker_search_cancer_markers (Type: CellMarkerTool)#

Search the CellMarker 2.0 database for cancer-context marker records with complete limit/offset p…

CellMarker_search_cancer_markers tool specification

Tool Information:

  • Name: CellMarker_search_cancer_markers

  • Type: CellMarkerTool

  • Description: Search the CellMarker 2.0 database for cancer-context marker records with complete limit/offset pagination and explicit total/has_more metadata. Cell-type phrase matching respects boundaries, so ‘T cell’ does not match ‘Fat cell’ or ‘Mast cell’. At least one of cancer_type, gene_symbol, or cell_type is required.

Parameters:

  • cancer_type (string) (optional) Cancer tissue type (e.g., ‘Breast’, ‘Lung’, ‘Brain’, ‘Liver’). Filters by tissue where cancer occurs.

  • gene_symbol (string) (optional) Marker gene to search in cancer context (e.g., ‘CD274’ for PD-L1, ‘EPCAM’)

  • cell_type (string) (optional) Cancer cell type to search for (e.g., ‘Cancer stem cell’, ‘T cell’, ‘Macrophage’)

  • limit ([‘integer’, ‘null’]) (optional) Maximum records to return. Default 200; total_records reports how many matched, so raise this or page with offset when it is larger.

  • offset ([‘integer’, ‘null’]) (optional) Records to skip before returning, for paging through total_records. Use data.next_offset for the next page.

Example Usage:

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