User Guide

active_score performs differential expression, reference-gamma unspliced excess calculation, optional bias correction, composite scoring, and stores results plus diagnostics. Downstream steps commonly include gene filtering with filter_active_genes, functional enrichment, and plotting.

The internal significant list uses strict thresholds. The complete results table is returned as all_results; use filter_active_genes for custom criteria. Diagnostics are available under adata_res.uns["scatrans"]["diagnostics"].

• Core Workflow
  • Run active_score (default parameters)
  • Gene filtering with filter_active_genes (core output tool)
  • diagnose_design
  • Layer names
• Functional Enrichment
  • run_gsea (pre-ranked GSEA)
  • run_kegg (convenience wrapper for KEGG pathways)
  • Using bundled gene sets
  • Using original Enrichr versions
  • simplify_enrichment (reduce redundant enrichment terms)
  • run_go (GO enrichment, clusterProfiler-style)
  • Exporting results
  • Additional enrichment plot options
• Visualization
  • Plotting style
  • Main plotting functions
• Optional Advanced Features
  • use_permutation=True
  • bias_correction
  • gamma_method and reference gamma robustness
  • show_effective_gamma=True
  • use_mixed_model=True + delta_variance
  • mode="advanced"
• Gene Feature Attachment & CLI
  • Command-line interface
• Standalone Differential Expression (no velocity data required)
  • Important: raw counts requirement