Package: SpliceImpactR 1.1.4

Zachary Wakefield

SpliceImpactR: An R package to identify functional impacts due to alternative RNA processing events

Works by taking in processed data from the HIT Index and/or rMATS and identifying how differentially used alternative RNA processing events lead to changes in protein function through various means. Primarily this is done through protein similarity, functional protein domain analysis, and domain-domain interaction changes. Notably, we both identify alterantive RNA processing event 'swaps' across condition and are able to perform holistic analyses regarding the impact of different RNA processing events.

Authors:Zachary Wakefield [cre, aut], Ana Fiszbein [aut]

SpliceImpactR_1.1.4.tar.gz
SpliceImpactR_1.1.4.zip(r-4.7-any)SpliceImpactR_1.1.4.zip(r-4.6-any)SpliceImpactR_1.1.4.zip(r-4.5-any)
SpliceImpactR_1.1.4.tgz(r-4.6-any)SpliceImpactR_1.1.4.tgz(r-4.5-any)
SpliceImpactR_1.1.4.tar.gz(r-4.7-any)SpliceImpactR_1.1.4.tar.gz(r-4.6-any)
SpliceImpactR_1.1.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpliceImpactR/json (API)

# Install 'SpliceImpactR' in R:
install.packages('SpliceImpactR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fiszbein-lab/spliceimpactr/issues

On BioConductor:SpliceImpactR-1.1.0(bioc 3.24)SpliceImpactR-1.0.0(bioc 3.23)

alternativesplicingdifferentialsplicingstatisticalmethodalignment

5.30 score 5 stars 6 scripts 276 downloads 58 exports 146 dependencies

Last updated from:52d46a9141. Checks:1 NOTE, 6 OK, 3 ERROR. Indexed: yes.

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bioc-checksNOTE256
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source / vignettesOK547
linux-releaseOK452
macos-releaseOK487
macos-oldrelOK414
windows-develERROR554
windows-releaseERROR612
windows-oldrelERROR657
wasm-releaseOK255

Exports:add_splice_partas_dt_from_s4as_splice_impact_resultattach_sequencescompare_hit_indexcompare_sequence_framecompare_sequences_alignmentcompare_transcript_pairsenrich_by_dbenrich_by_eventenrich_domains_hypergeofilter_spliceimpact_hitsget_annotationget_backgroundget_comprehensive_annotationsget_di_gene_enrichmentget_differential_inclusionget_domain_gene_for_enrichmentget_domainsget_enrichmentget_exon_featuresget_gene_enrichmentget_hitindexget_hits_coreget_hits_domainget_hits_final_viewget_hits_ppiget_hits_sequenceget_manual_featuresget_matched_events_chunkedget_pairsget_ppi_gene_enrichmentget_ppi_interactionsget_ppi_switchesget_protein_featuresget_proximal_shift_from_hitsget_ranked_pairsget_rmatsget_rmats_hitget_rmats_post_diget_splicing_impactget_user_dataget_user_data_post_diimport_di_tableintegrated_event_summarykeep_sig_pairsload_example_dataload_rmatsoverview_spicing_comparisonplot_alignment_summaryplot_di_volcano_dtplot_enriched_domains_countsplot_length_comparisonplot_ppi_summaryplot_two_transcripts_with_domains_unifiedprobe_individual_eventspliceimpact_s4_guidespliceimpact_s4_schema

Dependencies:abindAnnotationDbiaskpassbackportsBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootbroomcachemcarcarDatacigarilloclicodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivdoBydplyrfarverfastmapfilelockforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslpatchworkpbkrtestPFAM.dbpillarpkgconfigpngpolynomprettyunitsprogresspurrrpwalignquantregR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrestfulrRhtslibrjsonrlangRsamtoolsRSQLiterstatixrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXMLxml2XVectoryamlzoo

SpliceImpactR
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
Rendered fromSpliceImpactR.Rmdusingknitr::rmarkdown

Last update: 2026-10-09
Started: 2025-11-11

ORF-aware transcript-pair selection
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
Rendered fromtranscript_pair_ranking.Rmdusingknitr::rmarkdown

Last update: 2026-10-08
Started: 2026-10-08

Readme and manuals

Help Manual

Help pageTopics
Add one part to an existing SpliceImpactResultadd_splice_part
Convert S4 slots back to data.tableas_dt_from_s4
Build S4 SpliceImpact containeras_splice_impact_result
Attach transcript and protein sequences to an event or annotation tableattach_sequences
Compare HIT index values between conditionscompare_hit_index
Compare frame states after sequence alignmentcompare_sequence_frame
Compare isoform nucleotide and protein sequences by pairwise alignmentcompare_sequences_alignment
Compare user-selected transcript pairscompare_transcript_pairs
Run domain enrichment by databaseenrich_by_db
Run domain enrichment by event typeenrich_by_event
Domain-level enrichment via hypergeometric testenrich_domains_hypergeo
Filter a SpliceImpactResult by arbitrary paired-hit columnsfilter_spliceimpact_hits
Load and cache GENCODE annotations, sequences, and hybrid exon annotationsget_annotation
Build a transcript-pair background with domain and length annotationsget_background
Combine multiple sources of protein feature annotationsget_comprehensive_annotations
Extract Differential-Inclusion Genes for Enrichmentget_di_gene_enrichment
Differential Inclusion Analysis from Hit Index Tablesget_differential_inclusion
Extract Domain-Altering Genes for Enrichmentget_domain_gene_for_enrichment
Add protein domain annotations to splicing eventsget_domains
Gene Set Enrichment for Splicing-Linked Gene Listsget_enrichment
Map protein features to coding exonsget_exon_features
Unified gene selector for enrichment foregroundsget_gene_enrichment
Load HIT index PSI files for one or more samples/conditions.get_hitindex
Convenience accessor for core paired-hit columnsget_hits_core
Convenience accessor for domain-focused paired-hit columnsget_hits_domain
Access paired-hits as compact data.table subsetsget_hits_final_view
Convenience accessor for PPI-focused paired-hit columnsget_hits_ppi
Convenience accessor for sequence/frame-focused paired-hit columnsget_hits_sequence
Incorporate user-supplied protein featuresget_manual_features
Match splicing events to transcript annotations in chunksget_matched_events_chunked
Pair inclusion and exclusion forms of splicing eventsget_pairs
Extract Protein-Interaction-Affected Genes for Enrichmentget_ppi_gene_enrichment
Pull PPI from SpliceImpactR's dataget_ppi_interactions
Annotate hits_domain with PPI changes for inclusion vs exclusion formsget_ppi_switches
External function to fetch protein features from biomaRtget_protein_features
Classify splicing events as proximal or distalget_proximal_shift_from_hits
Jointly rank compatible transcript pairs by coding-region structureget_ranked_pairs
Expand rMATS event tables into scalar exon inclusion/exclusion coordinates.get_rmats
Wrapper function to get both rmats and hit index cleanlyget_rmats_hit
Import post-differential-inclusion rMATS resultsget_rmats_post_di
End-to-end SpliceImpactR wrapper with selectable output classget_splicing_impact
Get User-Supplied Splicing Event Dataget_user_data
Format user-supplied post-DI (post-differential-inclusion) splicing resultsget_user_data_post_di
Standardize a differential inclusion (DI) result tableimport_di_table
Integrated summary of event classification, alignment, and domain changesintegrated_event_summary
Filter event pairs by significance and deltaPSI thresholdskeep_sig_pairs
Load bundled example inputs for documentationload_example_data
Load rMATS event files into standardized data.tablesload_rmats
Overview of global splicing event distributions between conditionsoverview_spicing_comparison
Plot alignment score distribution and coding summaryplot_alignment_summary
Volcano plot for differential inclusion resultsplot_di_volcano_dt
Plot enriched domains by associated event countplot_enriched_domains_counts
Compare inclusion vs. exclusion isoform lengthsplot_length_comparison
Plot summary of altered PPI interactionsplot_ppi_summary
Plot two transcripts with exon structure and protein feature tracks (unified view)plot_two_transcripts_with_domains_unified
Visualize PSI values for a single splicing eventprobe_individual_event
Detailed guide for using SpliceImpactResultspliceimpact_s4_guide
S4 slot and key schema for SpliceImpactResultspliceimpact_s4_schema
SpliceImpact result container (S4)SpliceImpactResult-class