auto-Enrich documentation

AUTO-ENRICH:

• Quickstart
  • Installation
  • Minimal config example
  • Run command
  • Expected results
• Overview
• Module Index Reference
• Setup and Run
  • Pipeline Configuration File (config)
  • Possible Entry Points
  • Run Command
  • Behavior
  • Additional Flags
• Test data
  • Test 1 – Running Enrichment Analysis with Expression Dataset

Modules:

• Description
  • Module 1: Prepare Gene Lists
  • Module 2: Map Gene Identifiers
  • Module 3: gProfiler plus
  • Module 4: PANTHER plus
  • Module 5: Prepare GSEA inputs
  • Module 6: GSEA plus
  • Module 7: Filter EA results
• Outputs
  • Pipeline Outputs
  • Mapping and Annotations → /annotations
  • Module 1 → /prepared_gene_lists
  • Module 2 → /mapped_gene_lists
  • Modules 3 & 4 → /gprofiler & /panther
  • Modules 5 & 6: GSEA → /gsea
  • Module 7 → filter and /common_results

References:

• Credits
• References