Deseq2 Tools

Configuration File: deseq2_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the deseq2_tools.json configuration file.

Available Tools

run_deseq2_analysis (Type: DESeq2Tool)

Run R DESeq2 differential expression analysis on a count matrix + metadata. Returns gene counts, …

run_deseq2_analysis tool specification

Tool Information:

  • Name: run_deseq2_analysis

  • Type: DESeq2Tool

  • Description: Run R DESeq2 differential expression analysis on a count matrix + metadata. Returns gene counts, significance stats, and dispersion estimates. Uses actual R DESeq2 (not pydeseq2) for maximum accuracy. Supports custom design formulas, contrasts, reference levels, LFC shrinkage, and refit_cooks.

Parameters:

  • operation (string) (required) deseq2: differential expression, enrichgo: GO enrichment with clusterProfiler::simplify

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

  • metadata_file (string) (optional) Path to CSV metadata (samples x variables, must include design variables)

  • design (string) (optional) R formula string (e.g., ‘~ condition’, ‘~ Replicate + Media + Strain’)

  • contrast ([‘string’, ‘null’]) (optional) Contrast specification: ‘variable, level, reference’ (e.g., ‘Strain, 97, 1’)

  • ref_level ([‘string’, ‘null’]) (optional) Reference level: ‘variable, level’ (e.g., ‘condition, Control’)

  • alpha (number) (optional) Significance threshold (default: 0.05)

  • lfc_threshold (number) (optional) Log2 fold change threshold for filtering (default: 0 = no filter)

  • lfc_shrinkage (boolean) (optional) Apply apeglm LFC shrinkage (default: false)

  • refit_cooks (boolean) (optional) Refit Cook’s outliers (default: false)

  • gene_list_file ([‘string’, ‘null’]) (optional) For enrichgo: path to file with one gene ID per line

  • background_file ([‘string’, ‘null’]) (optional) For enrichgo: path to background gene list file

  • ontology (string) (optional) For enrichgo: GO ontology (BP, CC, MF). Default: BP

  • simplify_cutoff (number) (optional) For enrichgo: simplify similarity cutoff (default: 0.7)

  • id_type (string) (optional) Gene ID type (ENSEMBL, ENTREZID, SYMBOL). Default: ENSEMBL

  • organism (string) (optional) Organism annotation DB (org.Hs.eg.db, org.Mm.eg.db). Default: org.Hs.eg.db

Example Usage:

query = {
    "name": "run_deseq2_analysis",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)