Welcome to scAGDE’s documentation!

Contents:

• Installation
  • System Requirements
  • Installation Guide:
• Tutorial 1: End-to-end scATAC-seq analysis
  • 1. Read and preprocess data
  • 2. Setup and train scAGDE model
  • 3. Visualizing and evaluation
• Tutorial 2: Step-by-step scATAC-seq analysis
  • 1. Read and preprocess data
  • 2. Setup and train scAGDE model
  • 3. Visualizing and evaluation
• Tutorial 3: Imputation scATAC-seq analysis
  • 1. Read and preprocess data
  • 2. Setup and train scAGDE model
  • 3. The imputation visualization
  • 3. Downstream analysis
• Tutorial 4: Peak selection analysis
  • 1. Train scAGDE
  • 2. Further analysis (accessibility statistics and annotation)
• Tutorial 5: Batch-learning on large-scale dataset
  • 1. Read and preprocess data
  • 2. Setup and train scAGDE model
  • 3. Visualizing and evaluation