Timer Tools

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

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

Available Tools

TIMER2_gene_correlation (Type: TIMERTool)

Analyze Spearman correlation between two genes across TCGA cancer samples using cBioPortal data. …

TIMER2_gene_correlation tool specification

Tool Information:

  • Name: TIMER2_gene_correlation

  • Type: TIMERTool

  • Description: Analyze Spearman correlation between two genes across TCGA cancer samples using cBioPortal data. Returns correlation coefficient and p-value. Useful for identifying co-expressed genes in tumor microenvironment. Note: TIMER2.0/3.0 REST API is no longer public; uses cBioPortal as data source. Example: Correlate CD8A and PDCD1 expression in BRCA.

Parameters:

  • operation (string) (required) Operation type

  • cancer (string) (required) TCGA cancer type (e.g., ‘BRCA’, ‘LUAD’)

  • gene1 (string) (required) First gene symbol (e.g., ‘CD8A’)

  • gene2 (string) (required) Second gene symbol (e.g., ‘PDCD1’)

Example Usage:

query = {
    "name": "TIMER2_gene_correlation",
    "arguments": {
        "operation": "example_value",
        "cancer": "example_value",
        "gene1": "example_value",
        "gene2": "example_value"
    }
}
result = tu.run(query)

TIMER2_immune_estimation (Type: TIMERTool)

Estimate immune cell abundance in TCGA cancer samples using TIMER-equivalent marker gene expressi…

TIMER2_immune_estimation tool specification

Tool Information:

  • Name: TIMER2_immune_estimation

  • Type: TIMERTool

  • Description: Estimate immune cell abundance in TCGA cancer samples using TIMER-equivalent marker gene expression from cBioPortal. Returns infiltration proxies for 6 immune cell types (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, dendritic cells) using canonical marker genes (CD19, CD4, CD8A, FCGR3B, CD68, ITGAX). Note: TIMER2.0/3.0 REST API is no longer public; this tool uses cBioPortal TCGA data as a proxy.

Parameters:

  • operation (string) (required) Operation type

  • cancer (string) (required) TCGA cancer type abbreviation (e.g., ‘BRCA’, ‘LUAD’, ‘COAD’, ‘SKCM’, ‘GBM’)

  • gene ([‘string’, ‘null’]) (optional) Optional gene symbol to correlate with immune infiltration (e.g., ‘CD8A’, ‘PDCD1’)

Example Usage:

query = {
    "name": "TIMER2_immune_estimation",
    "arguments": {
        "operation": "example_value",
        "cancer": "example_value"
    }
}
result = tu.run(query)

TIMER2_survival_association (Type: TIMERTool)

Analyze overall survival association of gene expression in TCGA cancer patients using cBioPortal …

TIMER2_survival_association tool specification

Tool Information:

  • Name: TIMER2_survival_association

  • Type: TIMERTool

  • Description: Analyze overall survival association of gene expression in TCGA cancer patients using cBioPortal data. Performs log-rank test comparing high vs. low gene expression groups (median split). Returns log-rank p-value, median survival times, and event counts. Note: TIMER2.0/3.0 REST API is no longer public; uses cBioPortal TCGA data.

Parameters:

  • operation (string) (required) Operation type

  • cancer (string) (required) TCGA cancer type (e.g., ‘BRCA’, ‘LUAD’, ‘COAD’)

  • gene (string) (required) Gene symbol for survival analysis (e.g., ‘CD8A’, ‘TP53’, ‘BRCA1’)

Example Usage:

query = {
    "name": "TIMER2_survival_association",
    "arguments": {
        "operation": "example_value",
        "cancer": "example_value",
        "gene": "example_value"
    }
}
result = tu.run(query)