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🍑 PEACH

Getting Started

  • Installation
  • 🍑 PEACH Documentation

Tutorials

  • Tutorials
    • WORKFLOW 01: Data Loading & PCA Preprocessing
    • WORKFLOW 02: Hyperparameter Search with Cross-Validation
    • WORKFLOW 03: Archetypal Model Training
    • WORKFLOW 04: Archetype Coordinates & Cell Assignment
    • WORKFLOW 05: Gene & Pathway Enrichment Analysis
    • WORKFLOW 06: CellRank Integration for Lineage Analysis
    • WORKFLOW 08: Comprehensive Visualization
    • Tutorial 09: scATAC-seq Archetypal Analysis
    • Tutorial 10: Spatial Archetypal Analysis
  • WORKFLOW 01: Data Loading & PCA Preprocessing
  • WORKFLOW 02: Hyperparameter Search with Cross-Validation
  • WORKFLOW 03: Archetypal Model Training
  • WORKFLOW 04: Archetype Coordinates & Cell Assignment
  • WORKFLOW 05: Gene & Pathway Enrichment Analysis
  • WORKFLOW 06: CellRank Integration for Lineage Analysis
  • WORKFLOW 08: Comprehensive Visualization
  • Tutorial 09: scATAC-seq Archetypal Analysis
  • Tutorial 10: Spatial Archetypal Analysis

API Reference

  • API Reference
    • peach.pp
      • peach.pp.basic
    • peach.tl
      • peach.tl.archetypal
      • peach.tl.cellrank_integration
      • peach.tl.hyperparameters
      • peach.tl.spatial
      • peach.tl.statistical
    • peach.pl
      • peach.pl.archetypal
      • peach.pl.cellrank_viz
      • peach.pl.debug_dotplot
      • peach.pl.pattern_visualization
      • peach.pl.results
      • peach.pl.spatial
    • peach.pp.load_data
    • peach.pp.generate_synthetic
    • peach.pp.prepare_training
    • peach.pp.load_pathway_networks
    • peach.pp.compute_pathway_scores
    • peach.tl.train_archetypal
    • peach.tl.hyperparameter_search
    • peach.tl.archetypal_coordinates
    • peach.tl.assign_archetypes
    • peach.tl.extract_archetype_weights
    • peach.tl.compute_conditional_centroids
    • peach.tl.assign_to_centroids
    • peach.tl.gene_associations
    • peach.tl.pathway_associations
    • peach.tl.conditional_associations
    • peach.tl.pattern_analysis
    • peach.tl.archetype_exclusive_patterns
    • peach.tl.specialization_patterns
    • peach.tl.tradeoff_patterns
    • peach.tl.setup_cellrank
    • peach.tl.compute_lineage_pseudotimes
    • peach.tl.compute_lineage_drivers
    • peach.tl.compute_transition_frequencies
    • peach.tl.single_trajectory_analysis
    • peach.pl.archetypal_space
    • peach.pl.archetypal_space_multi
    • peach.pl.training_metrics
    • peach.pl.elbow_curve
    • peach.pl.archetype_positions
    • peach.pl.archetype_positions_3d
    • peach.pl.archetype_statistics
    • peach.pl.dotplot
    • peach.pl.pattern_dotplot
    • peach.pl.pattern_summary_barplot
    • peach.pl.pattern_heatmap
    • peach.pl.fate_probabilities
    • peach.pl.lineage_drivers
    • peach.tl.SearchConfig

Development

  • Contributing
  • Repository
  • Open issue

Python Module Index

p
 
p
- peach
    peach.pl
    peach.pl.archetypal
    peach.pl.cellrank_viz
    peach.pl.debug_dotplot
    peach.pl.pattern_visualization
    peach.pl.results
    peach.pl.spatial
    peach.pp
    peach.pp.basic
    peach.tl
    peach.tl.archetypal
    peach.tl.cellrank_integration
    peach.tl.hyperparameters
    peach.tl.spatial
    peach.tl.statistical

By Alexander Honkala

© Copyright 2026, Alexander Honkala.