Overview | Installation | Option 1: BiocManager | Option 2: devtools (GitHub) | External tools and acronyms | Workflow map | Load Reference Resources | Build Sample Manifest | Quick start wrapper (get_splicing_impact) | Read Splicing Events | Sample-Level QC and Exploration | Compare HITindex Between Conditions | PSI Distribution Overview | Differential Inclusion (DI) | Match Events to Sequences and Build Transcript Pairs | Legacy matcher | Sequence-Level Consequences | Domain-Level Changes and Domain Enrichment | PPI Rewiring | Gene Enrichment Foreground Probes | Visualize Transcript and Protein Consequences | Inspect a Single Event | Integrative Visualization | Output Description (hits_final, data, res) | hits_final (integrated event-level output) | data (raw sample-level input table) | res (differential inclusion output) | S4 Applications and Accessors | S4-first Main Workflow (Code Only) | Custom Input Entry Points | Add Manual Protein Features | Pre-DI Custom Table | Post-DI Custom Table | Post-DI rMATS Import | Transcript-Pair Entry Point | Session Info

Purpose and scope | Step 1: validate the input and establish the comparison | Step 2: build the reference index once | Step 3: require the candidate to represent its assigned form | Step 4: construct candidate pairs | Step 5: identify the event-specific region | Step 6: compare the coding region outside the event | Step 7: choose the pair transparently | Step 7b: fall back to an approximate pair | Step 8: inspect and analyze the result | Differences from the legacy protocol | Session information