add_splice_part         Add one part to an existing SpliceImpactResult
as_dt_from_s4           Convert S4 slots back to data.table
as_splice_impact_result
                        Build S4 SpliceImpact container
attach_sequences        Attach transcript and protein sequences to an
                        event or annotation table
compare_hit_index       Compare HIT index values between conditions
compare_sequence_frame
                        Compare frame states after sequence alignment
compare_sequences_alignment
                        Compare isoform nucleotide and protein
                        sequences by pairwise alignment
compare_transcript_pairs
                        Compare user-selected transcript pairs
enrich_by_db            Run domain enrichment by database
enrich_by_event         Run domain enrichment by event type
enrich_domains_hypergeo
                        Domain-level enrichment via hypergeometric test
filter_spliceimpact_hits
                        Filter a SpliceImpactResult by arbitrary
                        paired-hit columns
get_annotation          Load and cache GENCODE annotations, sequences,
                        and hybrid exon annotations
get_background          Build a transcript-pair background with domain
                        and length annotations
get_comprehensive_annotations
                        Combine multiple sources of protein feature
                        annotations
get_di_gene_enrichment
                        Extract Differential-Inclusion Genes for
                        Enrichment
get_differential_inclusion
                        Differential Inclusion Analysis from Hit Index
                        Tables
get_domain_gene_for_enrichment
                        Extract Domain-Altering Genes for Enrichment
get_domains             Add protein domain annotations to splicing
                        events
get_enrichment          Gene Set Enrichment for Splicing-Linked Gene
                        Lists
get_exon_features       Map protein features to coding exons
get_gene_enrichment     Unified gene selector for enrichment
                        foregrounds
get_hitindex            Load HIT index PSI files for one or more
                        samples/conditions.
get_hits_core           Convenience accessor for core paired-hit
                        columns
get_hits_domain         Convenience accessor for domain-focused
                        paired-hit columns
get_hits_final_view     Access paired-hits as compact data.table
                        subsets
get_hits_ppi            Convenience accessor for PPI-focused paired-hit
                        columns
get_hits_sequence       Convenience accessor for sequence/frame-focused
                        paired-hit columns
get_manual_features     Incorporate user-supplied protein features
get_matched_events_chunked
                        Match splicing events to transcript annotations
                        in chunks
get_pairs               Pair inclusion and exclusion forms of splicing
                        events
get_ppi_gene_enrichment
                        Extract Protein-Interaction-Affected Genes for
                        Enrichment
get_ppi_interactions    Pull PPI from SpliceImpactR's data
get_ppi_switches        Annotate hits_domain with PPI changes for
                        inclusion vs exclusion forms
get_protein_features    External function to fetch protein features
                        from biomaRt
get_proximal_shift_from_hits
                        Classify splicing events as proximal or distal
get_rmats               Expand rMATS event tables into scalar exon
                        inclusion/exclusion coordinates.
get_rmats_hit           Wrapper function to get both rmats and hit
                        index cleanly
get_rmats_post_di       Import post-differential-inclusion rMATS
                        results
get_splicing_impact     End-to-end SpliceImpactR wrapper with
                        selectable output class
get_user_data           Get User-Supplied Splicing Event Data
get_user_data_post_di   Format user-supplied post-DI
                        (post-differential-inclusion) splicing results
import_di_table         Standardize a differential inclusion (DI)
                        result table
integrated_event_summary
                        Integrated summary of event classification,
                        alignment, and domain changes
keep_sig_pairs          Filter event pairs by significance and deltaPSI
                        thresholds
load_example_data       Load bundled example inputs for documentation
load_rmats              Load rMATS event files into standardized
                        data.tables
overview_spicing_comparison
                        Overview of global splicing event distributions
                        between conditions
plot_alignment_summary
                        Plot alignment score distribution and coding
                        summary
plot_di_volcano_dt      Volcano plot for differential inclusion results
plot_enriched_domains_counts
                        Plot enriched domains by associated event count
plot_length_comparison
                        Compare inclusion vs. exclusion isoform lengths
plot_ppi_summary        Plot summary of altered PPI interactions
plot_two_transcripts_with_domains_unified
                        Plot two transcripts with exon structure and
                        protein feature tracks (unified view)
probe_individual_event
                        Visualize PSI values for a single splicing
                        event
spliceimpact_s4_guide   Detailed guide for using SpliceImpactResult
spliceimpact_s4_schema
                        S4 slot and key schema for SpliceImpactResult
SpliceImpactResult-class
                        SpliceImpact result container (S4)
