API Reference

• Trial Design
  • TrialDesign
  • Design Detection
• Statistical Methods
  • Difference-in-Differences
  • Bayesian DiD
  • Within-Arm and Between-Arm Comparisons
  • Cell-Type Abundance
  • Effect Sizes
  • Power Analysis
  • Mixed Effects Models
  • GSEA Integration
  • Pseudobulk Methods
  • Module Score Analysis
  • Time Series Analysis
  • Cross-Validation
  • Heterogeneity
  • Sensitivity
  • Survival Analysis
  • Diagnostics
  • Summary Utilities
  • Monte Carlo Simulation
• Scoring and Preprocessing
  • Gene-Set Scoring
  • Preprocessing
  • AnnData Tools
• Plotting
  • did_volcano_frame()
  • plot_abundance_interaction()
  • plot_did_forest()
  • plot_did_forest_interactive()
  • plot_did_volcano_interactive()
  • plot_gsea_heatmap()
  • plot_gsea_radar()
  • plot_module_umap_panel()
  • plot_parallel_trends()
  • plot_trial_dotplot()
  • plot_trial_interaction()
  • plot_trial_umap()
  • plot_trial_umap_panel()
  • plot_within_arm_comparison()
  • signed_logp()
• Datasets
  • categorize_celltype()
  • count_paired()
  • ensure_fdr()
  • harmonize_response()
  • load_aml()
  • load_cart()
  • load_sade_feldman()
  • load_stephenson_data()
  • load_vaccine_gse171964()
  • verify_paired_participants()
• Workflow and Analysis
  • Analysis Interfaces
  • Workflow API
  • Convenience Functions
• Benchmark Simulation
  • Simulator
  • Orchestrator
• Utilities and Validation
  • Utilities
  • Validation