Local junction variants (LJVs) | Variable-event selection | Variable-gene selection | Event-covariate association | Implementation

Table of Contents | Introduction | What Does Splikit Do? | How splikit get these data? | Installation | Prerequisites | Installation from Source | Verify Installation | Core Concepts | Splicing Junction Events | Matrix Representations | Coordinate Groups | Variable Event Detection | Getting Started | Quick Start Workflow | R6 Object-Oriented Interface | Creating a SplikitObject | Complete Workflow with Method Chaining | Step-by-Step Workflow | Subsetting SplikitObjects | Working with Existing Matrices | Accessing SplikitObject Fields | R6 vs Function-Based Interface Comparison | Performance Features | Main Workflow Functions | make_junction_ab() | make_m1() | make_m2() | Additional Data Processing Functions | make_gene_count() | make_velo_count() | Feature Selection Functions | find_variable_events() | find_variable_genes() | Utility Functions | get_pseudo_correlation() | get_rowVar() | get_silhouette_mean() | Complete Workflow Example | Scenario: Analyzing Cell Type-Specific Splicing | Advanced Workflow: Multi-sample Comparison | Advanced Usage | Performance Optimization | Parallel Processing | Memory Management | Integration with Other Packages | Seurat Integration | SingleCellExperiment Integration | Custom Analysis Functions | Differential Splicing Analysis | Troubleshooting | Common Issues and Solutions | Issue 1: Memory Errors with Large Datasets | Issue 2: STARsolo Directory Structure Problems | Issue 3: Barcode Mismatch Issues | Issue 4: Low Event Detection | Performance Benchmarking | Function Reference | Core Workflow Functions | Data Loading Functions | Technical Functions | Conclusion

Local junction variants (LJVs) | Variable-event selection | Variable-gene selection | Event-covariate association | Implementation

Table of Contents | Introduction | What Does Splikit Do? | How splikit get these data? | Installation | Prerequisites | Installation from Source | Verify Installation | Core Concepts | Splicing Junction Events | Matrix Representations | Coordinate Groups | Variable Event Detection | Getting Started | Quick Start Workflow | R6 Object-Oriented Interface | Creating a SplikitObject | Complete Workflow with Method Chaining | Step-by-Step Workflow | Subsetting SplikitObjects | Working with Existing Matrices | Accessing SplikitObject Fields | R6 vs Function-Based Interface Comparison | Performance Features | Main Workflow Functions | make_junction_ab() | make_m1() | make_m2() | Additional Data Processing Functions | make_gene_count() | make_velo_count() | Feature Selection Functions | find_variable_events() | find_variable_genes() | Utility Functions | get_pseudo_correlation() | get_rowVar() | get_silhouette_mean() | Complete Workflow Example | Scenario: Analyzing Cell Type-Specific Splicing | Advanced Workflow: Multi-sample Comparison | Advanced Usage | Performance Optimization | Parallel Processing | Memory Management | Integration with Other Packages | Seurat Integration | SingleCellExperiment Integration | Custom Analysis Functions | Differential Splicing Analysis | Troubleshooting | Common Issues and Solutions | Issue 1: Memory Errors with Large Datasets | Issue 2: STARsolo Directory Structure Problems | Issue 3: Barcode Mismatch Issues | Issue 4: Low Event Detection | Performance Benchmarking | Function Reference | Core Workflow Functions | Data Loading Functions | Technical Functions | Conclusion

Splicing-Pipeline | 1. Mapping using STARsolo

Splicing-Pipeline | 1. Mapping using STARsolo