Edger Limma Tools

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

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

Available Tools

RNAseq_edger_limma_de (Type: EdgeRLimmaTool)

Bulk RNA-seq differential expression via edgeR (QL-F) or limma-voom on a count matrix + sample me…

RNAseq_edger_limma_de tool specification

Tool Information:

  • Name: RNAseq_edger_limma_de

  • Type: EdgeRLimmaTool

  • Description: Bulk RNA-seq differential expression via edgeR (QL-F) or limma-voom on a count matrix + sample metadata — the two standard DE frameworks alongside DESeq2 (run_deseq2_analysis). method=’edger’ (good for small replicate counts) or ‘limma’ (large n / complex designs). Returns DEG counts at FDR-only, FDR+|logFC|, and strict (FDR+|logFC|+expression) filters, optional per-gene logFC/FDR, and the full ranked table on disk. Requires Rscript with Bioconductor edgeR + limma.

Parameters:

  • counts_file (string) (required) Path to counts CSV (genes x samples; first column = gene IDs)

  • metadata_file (string) (required) Path to sample metadata CSV (one row per sample)

  • design ([‘string’, ‘null’]) (optional) Design formula, e.g. ‘~ condition’ or ‘~ batch + condition’ (default ‘~ condition’)

  • contrast (string) (required) Contrast as ‘factor,level1,level2’ (tests level1 vs level2)

  • method (string) (required) DE framework: ‘edger’ (QL-F) or ‘limma’ (limma-voom)

  • lfc_threshold ([‘number’, ‘null’]) (optional) abs(logFC) threshold for the sig sets (default 0.5)

  • fdr_threshold ([‘number’, ‘null’]) (optional) FDR (adjusted p) threshold (default 0.05)

  • expr_threshold ([‘number’, ‘null’]) (optional) Expression threshold (logCPM/AveExpr) for the strict set (default 0)

  • exclude_samples ([‘string’, ‘null’]) (optional) Comma-separated sample IDs to drop before analysis

  • report_genes ([‘string’, ‘null’]) (optional) Comma-separated gene IDs to report individual logFC/FDR for

Example Usage:

query = {
    "name": "RNAseq_edger_limma_de",
    "arguments": {
        "counts_file": "example_value",
        "metadata_file": "example_value",
        "contrast": "example_value",
        "method": "example_value"
    }
}
result = tu.run(query)