Expression Anova Tools

Configuration File: expression_anova_tools.json Tool Type: Local Tools Count: 1

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

Available Tools

expression_anova_per_gene (Type: ExpressionANOVAPerGeneTool)

Per-gene ANOVA or log2 fold-change on a gene x sample expression matrix. Each gene contributes on…

expression_anova_per_gene tool specification

Tool Information:

  • Name: expression_anova_per_gene

  • Type: ExpressionANOVAPerGeneTool

  • Description: Per-gene ANOVA or log2 fold-change on a gene x sample expression matrix. Each gene contributes one value per group (its mean expression across group samples), then mode=’anova’ runs one-way ANOVA (f_oneway) across K groups of N gene-level means; mode=’fold_change’ computes per-gene log2((mean_a+1)/(mean_b+1)) between two groups and returns median/mean across genes. Use for gene-level comparisons across experimental conditions where each gene is treated as one observation (e.g. comparing strains, cell types, or treatments). Accepts CSV counts matrix (rows=genes, cols=samples) and CSV metadata (rows=samples with group_col). Auto-aligns by overlapping sample IDs (transposes counts if needed).

Parameters:

  • counts_file (string) (required) Path to CSV count matrix (genes x samples, first column = gene IDs).

  • meta_file (string) (required) Path to CSV metadata (rows=samples, contains group_col).

  • group_col (string) (required) Metadata column identifying groups (e.g. ‘Strain’, ‘cell_type’).

  • mode (string) (required) ‘anova’: one-way ANOVA across groups. ‘fold_change’: median per-gene log2FC between group_a and group_b.

  • exclude_groups ([‘array’, ‘null’]) (optional) Groups in group_col to exclude before analysis.

  • group_a ([‘string’, ‘null’]) (optional) Numerator group for fold_change mode.

  • group_b ([‘string’, ‘null’]) (optional) Denominator group for fold_change mode.

Example Usage:

query = {
    "name": "expression_anova_per_gene",
    "arguments": {
        "counts_file": "example_value",
        "meta_file": "example_value",
        "group_col": "example_value",
        "mode": "example_value"
    }
}
result = tu.run(query)