Tutorials

This section contains tutorials for using TMEformer’s In Silico Perturbation (ISP) capabilities.

Embedding-based ISP (isp_emb_sim):

• ISP Simulation Analysis Tutorial
  • Overview
  • Prerequisites
  • Step 1: Setup and Data Loading
  • Step 2: Load and Process ISP Results
  • Step 3: Statistical Analysis and Visualization
  • Interpretation
• TME Composition ISP Analysis Tutorial
  • Overview
  • TME Cell Types
  • Prerequisites
  • Step 1: Setup and Data Loading
  • Step 2: Load and Process ISP Results
  • Step 3: Visualization and Interpretation
  • Interpretation
• TME Rank ISP Analysis Tutorial
  • Overview
  • TME Cell Types
  • Prerequisites
  • Step 1: Setup and Data Loading
  • Step 2: Merge Background ISP Results
  • Step 3: Load and Process ISP Results
  • Step 4: Visualization and Interpretation
  • Interpretation

Gene Expression ISP (isp_gene_exp):

• Gene Expression Prediction Model Preparation and Training Tutorial
  • Overview
  • Prerequisites
  • Step 1: Prepare Fine-tuning Dataset
  • Step 2: Train GEP Model
  • Step 3: Prepare ISP Perturbation Dataset
  • Step 4: Prepare Background Gene Lists
• Gene Expression ISP Analysis Tutorial
  • Overview
  • Marker Gene Set (SET1)
  • Prerequisites
  • Step 1: Setup and Data Loading
  • Step 2: Load and Process ISP Results
  • Step 3: Statistical Analysis
  • Step 4: Visualization and Interpretation
  • Interpretation
• TME Composition ISP Analysis Tutorial (Gene Expression Prediction)
  • Overview
  • TME Cell Types
  • Marker Gene Set (SET1)
  • Prerequisites
  • Step 1: Setup and Data Loading
  • Step 2: Load and Process ISP Results
  • Step 3: Calculate Z-scores
  • Step 4: Visualization and Interpretation
  • Interpretation
• TME Rank ISP Analysis Tutorial (Gene Expression Prediction)
  • Overview
  • TME Cell Types
  • Marker Gene Set (SET1)
  • Prerequisites
  • Step 1: Setup and Data Loading
  • Step 2: Load and Process ISP Results
  • Step 3: Statistical Analysis
  • Step 4: Visualization and Interpretation
  • Interpretation