Scvitools-Docs-Truly-Complete Skill

Comprehensive assistance with scvi-tools development, generated from official documentation covering deep probabilistic models for single-cell analysis.

When to Use This Skill

This skill should be triggered when:

Core scvi-tools Usage

• Data Loading: Reading or processing single-cell data (h5ad, csv,loom, 10x formats)
• Model Training: Setting up or training scVI, totalVI, MultiVI, scANVI, etc.
• Data Integration: Batch correction, cross-study integration, label transfer
• Multi-modal Analysis: CITE-seq, ATAC-seq, spatial transcriptomics data
• Differential Analysis: DE testing, trajectory inference, perturbation analysis

Advanced Modeling

• Custom Models: Building probabilistic modules, custom data loaders
• Hyperparameter Tuning: Using autotune module, Ray integration
• Model Hub: Uploading/downloading pretrained models
• Training Optimization: Multi-GPU training, callbacks, minification

Development Tasks

• API Implementation: Using core modules, distributions, neural networks
• Extension Development: Creating external models, custom training plans
• Data Pipeline: AnnData management, field validation, registry systems

Quick Reference

Essential Data Operations

Load PBMC CITE-seq dataset

import scvi
adata = scvi.data.pbmc_seurat_v4_cite_seq()

Read h5ad files with backing

adata = scvi.data.read_h5ad("data.h5ad", backed="r")

Generate synthetic test data

adata = scvi.data.synthetic_iid(
    n_genes=100,
    n_batches=2,
    n_labels=3,
    return_mudata=False
)

Core Model Setup

Setup SCVI model

scvi.model.SCVI.setup_anndata(
    adata,
    layer="counts",
    batch_key="batch",
    labels_key="cell_type"
)
model = scvi.model.SCVI(adata)

Train and extract latent space

model.train(max_epochs=100)
latent = model.get_latent_representation()
adata.obsm["X_scVI"] = latent

Save and load models

model.save("my_model.pt")
loaded_model = scvi.model.SCVI.load("my_model.pt")

Advanced Model Operations

Setup MultiVI for multi-modal data

scvi.model.MULTIVI.setup_anndata(
    adata,
    layer="counts",
    protein_expression_obsm_key="protein_expression",
    batch_key="batch"
)
model = scvi.model.MULTIVI(adata)

Differential expression analysis

de_results = model.differential_expression(
    groupby="cell_type",
    group1="CD4 T cells",
    group2="CD8 T cells"
)

Hyperparameter tuning with autotune

import ray.tune as tune
search_space = {
    "model_params": {
        "n_hidden": tune.choice([64, 128, 256]),
        "n_layers": tune.choice([1, 2, 3])
    },
    "train_params": {
        "max_epochs": 100,
        "plan_kwargs": {"lr": tune.loguniform(1e-4, 1e-2)}
    }
}

results = scvi.autotune.run_autotune(
    scvi.model.SCVI,
    data=adata,
    mode="min",
    metrics="validation_loss",
    search_space=search_space,
    num_samples=5
)

Model Hub Operations

Download pretrained model

hub_model = scvi.hub.HubModel.pull_from_huggingface_hub("scvi-tools/model-name")
model = hub_model.load_model()

Upload model to hub

metadata = scvi.hub.HubMetadata.from_dir("./model_dir", "0.8.0")
hub_model = scvi.hub.HubModel(local_dir="./model_dir", metadata=metadata)
hub_model.push_to_huggingface_hub("my-username/my-model")

Data Field Management

Access MuData layer fields

from scvi.data.fields import MuDataLayerField
field = MuDataLayerField(attr_name="layers", attr_key="counts", mod_key="rna")
registry_key = field.registry_key

Use collection adapter for large datasets

from scvi.dataloaders import CollectionAdapter
adapter = CollectionAdapter(anndata_collection)

Reference Files

Core API Documentation

• core_api_data.md: Data loading utilities (68 pages) - scvi.data.* modules for reading various single-cell formats, synthetic data generation, and data field management
• core_api_distributions.md: Probability distributions (6 pages) - JAX-based distributions like JaxNegativeBinomialMeanDisp for probabilistic modeling
• core_api_hub.md: Model hub functionality (3 pages) - scvi.hub.* for uploading/downloading pretrained models via HuggingFace
• core_api_models.md: Model implementations - Comprehensive coverage of all scvi-tools models (SCVI, totalVI, MultiVI, etc.)
• core_api_modules.md: Neural network modules - VAE architectures, encoders/decoders, and probabilistic modules
• core_api_neural_networks.md: Neural network components - scvi.nn.* building blocks for custom architectures
• core_api_training.md: Training infrastructure - Training plans, callbacks, trainers, and optimization utilities
• core_api_utils.md: Utility functions - Helper functions and miscellaneous utilities

User Guides

• user_guide_overview.md: High-level introduction to scvi-tools concepts and architecture
• user_guide_models.md: Detailed model documentation and usage patterns
• user_guide_use_cases.md: Common workflows and practical applications

Tutorials

• tutorials_quick_start.md: Getting started guides and basic workflows
• tutorials_scrna.md: Single-cell RNA-seq specific tutorials (integration, DE, labeling)
• tutorials_multimodal.md: Multi-modal analysis (CITE-seq, MultiVI, totalVI)
• tutorials_spatial.md: Spatial transcriptomics analysis (gimVI, Tangram, Cell2location)
• tutorials_atac.md: ATAC-seq analysis (PeakVI, scBasset, PoissonVI)
• tutorials_cytometry.md: Flow cytometry and mass cytometry data (CytoVI)
• tutorials_r.md: R integration with reticulate package
• tutorials_hub.md: Model hub usage and deployment
• tutorials_use_cases.md: Specific use case examples and best practices
• tutorials_advanced.md: Advanced techniques and custom model development

Development Resources

• developer_docs.md: Core development documentation and architecture
• external_models.md: External model integrations and extensions
• installation_getting_started.md: Setup and installation instructions
• other.md: Additional resources and references

Working with This Skill

For Beginners

1. Start with tutorials_quick_start.md for basic scvi-tools workflows
2. Use tutorials_scrna.md for standard single-cell RNA-seq analysis
3. Reference core_api_data.md for data loading and preprocessing
4. Follow user_guide_overview.md to understand core concepts

For Intermediate Users

1. Explore tutorials_multimodal.md for CITE-seq and multi-modal analysis
2. Use tutorials_spatial.md for spatial transcriptomics applications
3. Reference core_api_models.md for advanced model configurations
4. Consult tutorials_use_cases.md for specific workflow patterns

For Advanced Users

1. Study developer_docs.md for extending scvi-tools
2. Use tutorials_advanced.md for custom model development
3. Reference core_api_training.md for training optimization
4. Explore external_models.md for integration with other tools

Navigation Tips

• Quick model reference: Check core_api_models.md for model-specific parameters
• Data format help: Core_api_data.md covers all supported input formats
• Training issues: Core_api_training.md has troubleshooting and optimization guides
• Integration patterns: Tutorials_multimodal.md and tutorials_spatial.md for complex data types
• Development guidance: Developer_docs.md for architectural understanding

Key Concepts

Core Models

• SCVI: Single-cell Variational Inference for scRNA-seq integration
• totalVI: Total Variational Inference for joint RNA+protein analysis
• MultiVI: Multi-modal Variational Inference for paired/unpaired data
• scANVI: Semi-supervised SCVI for cell type annotation
• PeakVI: Variational inference for scATAC-seq peak analysis

Data Structures

• AnnData: Primary data structure for single-cell data
• MuData: Multi-modal data container for multiple assays
• Data Registry: Internal mapping of data fields to model inputs
• Fields: Data accessors for different AnnData/MuData attributes

Training Infrastructure

• Training Plans: PyTorch Lightning modules for different model types
• Autotune: Ray Tune integration for hyperparameter optimization
• Callbacks: Training monitoring and early stopping utilities
• Hub: Model sharing and deployment platform

Probabilistic Components

• VAE: Variational Autoencoder base architecture
• Distributions: Custom probability distributions for count data
• Modules: Neural network components and probabilistic layers
• Inference: Posterior approximation and variational inference methods

Resources

Quick Access

• Model selection: Use model-specific tutorials for guidance on choosing appropriate models
• Data preparation: Core_api_data.md for format-specific loading instructions
• Troubleshooting: Developer docs and training guides for common issues
• Examples: All tutorials contain runnable code examples with real datasets

Development

• External contributions: Developer docs provide guidelines for extending scvi-tools
• API reference: Core API documentation for all public interfaces
• Architecture: Understanding the modular structure for custom development

Notes

• This skill provides comprehensive coverage of scvi-tools v1.3.3 documentation
• All code examples are extracted from official tutorials and API documentation
• Reference files maintain original structure with complete examples and parameter descriptions
• Skill is optimized for both beginners learning scvi-tools and experts implementing advanced analyses

Updating

To refresh this skill with updated documentation:

1. Re-run the documentation scraper with the current scvi-tools version
2. Update reference files with new API changes and tutorials
3. Verify code examples against the latest release
4. Test all patterns for compatibility with new versions