Gdc Tools¶

Configuration File: gdc_tools.json Tool Type: Local Tools Count: 7

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

Available Tools¶

GDC_get_cnv_data (Type: GDCCNVTool)¶

Query copy number variation (CNV) files from GDC/TCGA projects. Returns CNV segment and gene-leve


GDC_get_cnv_data tool specification

Tool Information:

  • Name: GDC_get_cnv_data

  • Type: GDCCNVTool

  • Description: Query copy number variation (CNV) files from GDC/TCGA projects. Returns CNV segment and gene-level copy number files. Use for amplification/deletion analysis.

Parameters:

  • project_id (string) (required) GDC project (e.g., ‘TCGA-BRCA’)

  • gene_symbol (string) (optional) Optional: Gene symbol to focus analysis

  • size (integer) (optional) Number of results

Example Usage:

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

GDC_get_gene_expression (Type: GDCGeneExpressionTool)¶

Query RNA-Seq gene expression files from GDC/TCGA projects. Returns file metadata for expression 


GDC_get_gene_expression tool specification

Tool Information:

  • Name: GDC_get_gene_expression

  • Type: GDCGeneExpressionTool

  • Description: Query RNA-Seq gene expression files from GDC/TCGA projects. Returns file metadata for expression quantification data. Use to find expression data for downstream analysis.

Parameters:

  • project_id (string) (required) GDC project (e.g., ‘TCGA-BRCA’, ‘TCGA-LUAD’, ‘TCGA-GBM’)

  • gene_id (string) (optional) Optional: Ensembl gene ID (e.g., ‘ENSG00000141510’ for TP53)

  • size (integer) (optional) Number of results

Example Usage:

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

GDC_get_mutation_frequency (Type: GDCMutationFrequencyTool)¶

Get mutation frequency statistics for a gene across all TCGA cancers. Returns SSM case count, CNV


GDC_get_mutation_frequency tool specification

Tool Information:

  • Name: GDC_get_mutation_frequency

  • Type: GDCMutationFrequencyTool

  • Description: Get mutation frequency statistics for a gene across all TCGA cancers. Returns SSM case count, CNV gain/loss cases. Answers ‘How often is this gene mutated?’

Parameters:

  • gene_symbol (string) (required) Gene symbol (e.g., ‘TP53’, ‘KRAS’, ‘EGFR’)

Example Usage:

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

GDC_get_ssm_by_gene (Type: GDCSSMTool)¶

Get somatic mutations (SSMs) for a gene across TCGA/GDC projects. Returns mutation type, genomic 


GDC_get_ssm_by_gene tool specification

Tool Information:

  • Name: GDC_get_ssm_by_gene

  • Type: GDCSSMTool

  • Description: Get somatic mutations (SSMs) for a gene across TCGA/GDC projects. Returns mutation type, genomic coordinates, and amino acid changes. Essential for pan-cancer mutation analysis.

Parameters:

  • gene_symbol (string) (required) Gene symbol (e.g., ‘TP53’, ‘EGFR’, ‘BRAF’, ‘KRAS’)

  • project_id (string) (optional) Optional: Filter by project (e.g., ‘TCGA-BRCA’, ‘TCGA-LUAD’)

  • size (integer) (optional) Number of results (1–100)

Example Usage:

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

GDC_list_files (Type: GDCFilesTool)¶

List GDC files filtered by data_type and other fields. Use to identify downloadable artifacts (e
.

GDC_list_files tool specification

Tool Information:

  • Name: GDC_list_files

  • Type: GDCFilesTool

  • Description: List GDC files filtered by data_type and other fields. Use to identify downloadable artifacts (e.g., expression quantification) for analysis pipelines.

Parameters:

  • data_type (string) (optional) Data type filter (e.g., ‘Gene Expression Quantification’).

  • size (integer) (optional) Number of results (1–100).

  • offset (integer) (optional) Offset for pagination (0-based).

Example Usage:

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

GDC_list_projects (Type: GDCProjectsTool)¶

List GDC projects (TCGA, TARGET, etc.) with case/file counts. Use to discover available cancer co


GDC_list_projects tool specification

Tool Information:

  • Name: GDC_list_projects

  • Type: GDCProjectsTool

  • Description: List GDC projects (TCGA, TARGET, etc.) with case/file counts. Use to discover available cancer cohorts and their data volume. Filter by program (TCGA, TARGET, CGCI, etc.).

Parameters:

  • program (string) (optional) Filter by program name (e.g., ‘TCGA’, ‘TARGET’)

  • size (integer) (optional) Number of results (1–100)

Example Usage:

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

GDC_search_cases (Type: GDCCasesTool)¶

Search cancer cohort cases in NCI GDC by project and filters. Use to retrieve case-level metadata


GDC_search_cases tool specification

Tool Information:

  • Name: GDC_search_cases

  • Type: GDCCasesTool

  • Description: Search cancer cohort cases in NCI GDC by project and filters. Use to retrieve case-level metadata for cohort construction and downstream file queries.

Parameters:

  • project_id (string) (optional) GDC project identifier (e.g., ‘TCGA-BRCA’).

  • size (integer) (optional) Number of results (1–100).

  • offset (integer) (optional) Offset for pagination (0-based).

Example Usage:

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