Tutorials

We provide a variety of tutorials to help you get started with scXpand:

• Predicting T Cell Expansion from scRNA-seq Data - Download example scRNA-seq dataset (with no paired TCR-seq) and apply scXpand models for T cell expansion prediction using a breast cancer dataset example.

• Preparing Training Data from Paired scRNA/TCR-seq - Complete pipeline for preparing labeled data (expansion status and tissue type) from paired scRNA/TCR-seq data, including quality control, MAGIC imputation, automatic cutoff determination for cell type classification, and expansion labeling.

• Model Inference and Evaluation Pipeline - Load trained models, run inference on labeled data, and evaluate performance using ROC curves and AUROC metrics across different tissue types and labels.

• Autoencoder Embedding Visualization - Generate and visualize latent representations from autoencoder models, coloring plots by expansion status and tissue type for biological insights.

• Predicting T Cell Expansion from scRNA-seq Data
• Preparing Training Data from Paired scRNA/TCR-seq
• Model Inference & Evaluation Pipeline
• Embedding Visualization