Introduction | Installation | Data Structure and Input Format | Input File Format | Processing Multiple Files | Recommended File Path Structure | Recommended Naming Convention | Language Compatibility | Example Input File | Core functions | Example Workflow | Step 1: Load and Process PDF Files | Step 2: Extract Text from PDFs | Step 3: Extract Key Information from Text | Step 4: Extract Additional Information | Step 5: Extract Genetic Mutation Data | Step 6: Identify Gene Fusions | Step 7: Search for Pathogenicity Information | Step 8: Filter Pathogenic Mutations | Step 9: Classify Biopsies | Step 10: Extract Chip Identifier | Additional Features | Shiny App | Conclusion