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
fadvi
Python Module Index
Python Module Index
f
f
fadvi
fadvi._fadvae
