scxpand 0.3.4

Pan-cancer detection of T-cell clonal expansion from single-cell RNA sequencing

scXpand: Pan-cancer Detection of T-cell Clonal Expansion

Detect T-cell clonal expansion from single-cell RNA sequencing data without paired TCR sequencing

Documentation • Installation • Quick Start • Usage Guide • Citation

A framework for predicting T-cell clonal expansion from single-cell RNA sequencing data.

Manuscript in preparation - detailed methodology and benchmarks coming soon.

View full documentation for comprehensive guides and API reference.

Features

• Multiple Model Architectures:
  • Autoencoder-based: Encoder-decoder with reconstruction and classification heads
  • MLP: Multi-layer perceptron
  • LightGBM: Gradient boosted decision trees
  • Linear Models: Logistic regression and support vector machines
• Scalable Processing: Handles millions of cells with memory-efficient data streaming from disk during training
• Automated Hyperparameter Optimization: Built-in Optuna integration for model tuning

Installation

This section explains the two ways to install scXpand:

• Installing the Published Package: For regular use.
• Local Development Setup: For contributing or working with the source code.

Installing the Published Package

scXpand is available in two variants to match your hardware:

If you have an NVIDIA GPU with CUDA support:

• With plain pip (add CUDA index):

  pip install --upgrade scxpand-cuda --extra-index-url https://download.pytorch.org/whl/cu128
  

• With uv:

  uv pip install --upgrade scxpand-cuda --extra-index-url https://download.pytorch.org/whl/cu128 --index-strategy unsafe-best-match
  

Otherwise (CPU, Apple Silicon, or non-CUDA GPUs):

• With plain pip:

  pip install --upgrade scxpand
  

• With uv:

  uv pip install --upgrade scxpand
  

See the full installation guide for detailed setup instructions.

---

Local Development Setup

If you want to contribute or work with the latest source code, follow these steps:

1. Clone the repository:

   git clone https://github.com/yizhak-lab-ccg/scXpand.git
   cd scXpand
   

2. Run the install script:

   • Windows PowerShell:

     .\install.bat
     

   • macOS/Linux:

     ./install.sh
     

For more details, refer to the installation guide.

Quick Start

import scxpand
# Make sure that "your_data.h5ad" includes only T cells for the results to be meaningful
# Ensure that "your_data.var_names" are provided as Ensembl IDs (as the pre-trained models were trained using this gene representation)
# Please refer to our documentation for more information

# List available pre-trained models
scxpand.list_pretrained_models()

# Run inference with automatic model download
results = scxpand.run_inference(
    model_name="pan_cancer_autoencoder",  # default model
    data_path="your_data.h5ad"
)

# Access predictions
predictions = results.predictions
if results.has_metrics:
    print(f"AUROC: {results.get_auroc():.3f}")

Documentation

See our Tutorial Notebook for a complete example with data preprocessing, T-cell filtering, gene ID conversion, and model application using a real breast cancer dataset.

Setup & Getting Started:

• Installation Guide - Setup for local development of scXpand
• User Guide - Quick start and comprehensive workflow guide
• Data Format - Input data requirements and specifications

Using Pre-trained Models:

• Model Inference - Run predictions on new data with pre-trained models

Training Your Own Models:

• Model Training - Train models with CLI and programmatic API
• Hyperparameter Optimization - Automated model tuning with Optuna

Understanding Results:

• Model Architectures - Detailed architecture descriptions and configurations
• Evaluation Metrics - Performance assessment and interpretation
• Output Format - Understanding model outputs and results

📖 Full Documentation - Complete guides, API reference, and interactive tutorials

License

This project is licensed under the MIT License – see the LICENSE file for details.

Citation

If you use scXpand in your research, please cite:

@article{scxpand2025,
  title={scXpand: Pan-cancer detection of T-cell clonal expansion from single-cell RNA sequencing without paired single-cell TCR sequencing},
  author={[Your Name]},
  journal={[Journal Name]},
  year={2025},
  doi={[DOI]}
}

This project was created in favor of the scientific community worldwide, with a special dedication to the cancer research community. We hope you’ll find this repository helpful, and we warmly welcome any requests or suggestions - please don’t hesitate to reach out!