Welcome to Starfysh’s documentation!

Basics:

• Overview
  • Features
  • Model Specifications
  • I/O
• Installation
• Quickstart

Examples:

• Starfysh tutorial on simulated ST dataset
  • Load starfysh
    • (1). load data and marker genes:
    • (2). Preprocessing (finding anchor spots)
    • (3). Optional: Archetypal Analysis
  • Run starfysh
    • (1). Model parameters
    • (2). Model training
    • (3). Downstream analysis
  • Save model & inferred parameters
• Starfysh tutorial on real dataset
  • Overview
  • Load starfysh
    • (1). load data and marker genes
    • (2). Preprocessing (finding anchor spots)
    • (3). Optional: Archetypal Analysis
  • Run starfysh
    • (1). Model parameters
    • (2). Model training
    • (3). Downstream analysis
  • Save model & inferred parameters

API Reference:

• starfysh package
  • Submodules
  • starfysh.AA module
    • ArchetypalAnalysis
  • starfysh.dataloader module
    • VisiumDataset
    • VisiumPoEDataSet
  • starfysh.plot_utils module
    • pl_spatial_inf_feature()
    • pl_spatial_inf_gene()
    • pl_umap_feature()
    • plot_anchor_spots()
    • plot_evs()
    • plot_spatial_feature()
    • plot_spatial_gene()
  • starfysh.post_analysis module
    • create_corr_network_5()
    • display_reconst()
    • gene_mean_vs_inferred_prop()
    • get_LISA()
    • get_Moran()
    • get_SCI()
    • get_adata()
    • get_cormtx()
    • get_corr_map()
    • get_factor_dist()
    • get_hub_cormtx()
    • get_z_umap()
    • plot_density()
    • plot_stacked_prop()
    • plot_type_all()
  • starfysh.starfysh module
    • AVAE
    • AVAE_PoE
    • NegBinom
    • model_ct_exp()
    • model_eval()
    • train()
    • train_poe()
    • valid_model()
  • starfysh.utils module
    • VisiumArguments
    • append_sigs()
    • extract_feature()
    • filter_gene_sig()
    • get_adata_wsig()
    • get_alpha_min()
    • get_anchor_spots()
    • get_simu_map_info()
    • get_umap()
    • get_windowed_library()
    • init_weights()
    • load_adata()
    • load_signatures()
    • preprocess()
    • preprocess_img()
    • refine_anchors()
    • run_starfysh()
  • Module contents

Indices and tables

• Index

• Module Index

• Search Page