scAtlasVAE
  • Introduction
  • Preprocessing Immune Profiling Data
  • Automatic transfer to pan-disease CD8+ T cell atlas
  • Integrating Multi-source Gene Expression (GEX)
  • Transfering Multi-source Gene Expression (GEX)
  • Re-Training Gene Expression (GEX)
  • API
scAtlasVAE
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Welcome to scAtlasVAE’s documentation!

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Contents

  • Introduction
    • Installation
      • PyTorch installation
    • Tutorial
      • Basic Usage
    • Key functionality
    • Model architecture
  • Preprocessing Immune Profiling Data
  • Automatic transfer to pan-disease CD8+ T cell atlas
    • Step1: Load the reference and query data
    • Step2: Transfer the cell type annotation
    • Step3: Transfer the higher-resolution cell type annotation for Tex
  • Integrating Multi-source Gene Expression (GEX)
    • Training the VAE model using batch key
    • Training the VAE model using batch key and categorical covariates (e.g. study_name)
    • Training the VAE model using batch key and label key (e.g. cell_type)
    • Training the VAE model using multiple batch keys and mutiple label keys
    • Saving the VAE model
  • Transfering Multi-source Gene Expression (GEX)
    • Transfer without training query datasets with reference datasets
      • Getting the transfered latent embedding
      • Mapping the UMAP representation to the reference
    • Transfer by training query datasets with reference datasets
  • Re-Training Gene Expression (GEX)
  • API
    • Preprocessing
      • VDJPreprocessingV1Human
        • VDJPreprocessingV1Human.process()
      • VDJPreprocessingV1Mouse
        • VDJPreprocessingV1Mouse.process()
    • Model
      • scAtlasVAE
      • scAtlasVAE’s Methods table
      • scAtlasVAE’s Methods
        • scAtlasVAE.partial_load_state_dict()
        • scAtlasVAE.get_config()
        • scAtlasVAE.save_to_disk()
        • scAtlasVAE.load_from_disk()
        • scAtlasVAE.setup_anndata()
        • scAtlasVAE.fit()
    • Pipeline
      • pipeline.run_transfer()
    • Tools
      • umap_alignment()
      • cell_type_alignment()
    • Utilities
      • get_default_device()
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