fadvi

Contents:

  • Installation
    • Requirements
    • Installation Methods
      • From PyPI (Recommended)
      • From Source
    • Verify Installation
    • GPU Support
  • Tutorials
    • Quick Start Guide
      • Installation
      • Basic Usage
      • Next Steps
    • Basic Usage
      • Understanding FADVI
        • Key Concepts
      • Data Preparation
        • Preparing AnnData Object
      • Model Initialization
        • Basic Setup
        • Advanced Configuration
      • Training the Model
        • Basic Training
        • Custom Training
      • Getting Results
        • Latent Representation
        • Batch and Label Predictions
      • Downstream Analysis
        • Visualization
        • Quality Assessment
      • Saving and Loading Models
        • Save Model
        • Load Model
      • Next Steps
    • Advanced Usage
      • Custom Loss Functions
      • Starting with reference data and query data
      • Integration with scvi-tools Ecosystem
      • Custom Data Splitting
      • Export for Other Tools
      • Interpretability Analysis
        • Prerequisites
        • Basic Interpretability Usage
        • Label Prediction Interpretability
        • Available Attribution Methods
        • Working with Attribution Results
        • Soft Predictions with Interpretability
        • Batch Processing for Large Datasets
        • Visualization and Analysis
      • Next Steps
    • Integrating Spatial Transcriptomics and Single-Cell Data
      • What input ST data should be used?
        • Can I use unlabeled ST data?
      • (Recommended) Integrating labeled ST data with scRNA-seq data
        • Annotating ST data with TACCO
        • FADVI integration
      • (Alternative) Integrating unlabeled ST data with scRNA-seq data
      • Next Steps
  • Examples & Demos
    • Benchmarking FADVI with other methods on Single-Cell Immune Atlas
      • Set up and data loading
      • Batch integration
        • FADVI training: supervised.
        • FADVI training: semi-supervised.
        • FADVI training: unsupervised.
      • UMAP visualization
      • Benchmarking using scib_metrics
  • API Reference
    • Main Classes
      • fadvi.FADVI
        • FADVI
      • fadvi.FADVAE
        • FADVAE
  • Contributing to FADVI
    • Getting Started
      • Development Setup
    • Types of Contributions
      • Bug Reports
      • Feature Requests
      • Code Contributions
    • Development Workflow
    • Code Standards
      • Style Guide
      • Documentation
      • Testing
    • Pull Request Process
      • Pull Request Template
    • Code Review Process
    • Release Process
    • Community Guidelines
    • Getting Help
    • Recognition
  • Changelog
    • [Released]
    • [0.2.0] - 2025-11-04
      • Added
      • Improved
      • Technical
      • Dependencies
    • [0.1.0.post1] - 2025-09-12
      • Added
      • Technical
    • [Unreleased]
    • [0.1.0] - 2025-09-09
      • Added
      • Features
      • Technical
      • Documentation
      • Testing
      • Known Issues
      • Dependencies
    • [0.0.1] - 2025-09-04
      • Added
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© Copyright 2025, Wendao Liu.

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