Package: SpliceImpactR 1.1.0

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_1.1.0.tar.gz
SpliceImpactR_1.1.0.zip(r-4.7)SpliceImpactR_1.1.0.zip(r-4.6)SpliceImpactR_1.1.0.zip(r-4.5)
SpliceImpactR_1.1.0.tgz(r-4.6-any)SpliceImpactR_1.1.0.tgz(r-4.5-any)
SpliceImpactR_1.1.0.tar.gz(r-4.7-any)SpliceImpactR_1.1.0.tar.gz(r-4.6-any)
SpliceImpactR_1.1.0.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)

alternativesplicing differentialsplicing statisticalmethod alignment

4.48 score 2 stars 3 scripts 57 exports 144 dependencies

Last updated from:64b59abd29. Checks:1 NOTE, 6 OK, 3 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	309
linux-devel-x86_64	OK	531
source / vignettes	OK	489
linux-release-x86_64	OK	636
macos-release-arm64	OK	310
macos-oldrel-arm64	OK	287
windows-devel	ERROR	408
windows-release	ERROR	419
windows-oldrel	ERROR	425
wasm-release	OK	294

Exports:add_splice_part as_dt_from_s4 as_splice_impact_result attach_sequences compare_hit_index compare_sequence_frame compare_sequences_alignment compare_transcript_pairs enrich_by_db enrich_by_event enrich_domains_hypergeo filter_spliceimpact_hits get_annotation get_background get_comprehensive_annotations get_di_gene_enrichment get_differential_inclusion get_domain_gene_for_enrichment get_domains get_enrichment get_exon_features get_gene_enrichment get_hitindex get_hits_core get_hits_domain get_hits_final_view get_hits_ppi get_hits_sequence get_manual_features get_matched_events_chunked get_pairs get_ppi_gene_enrichment get_ppi_interactions get_ppi_switches get_protein_features get_proximal_shift_from_hits get_rmats get_rmats_hit get_rmats_post_di get_splicing_impact get_user_data get_user_data_post_di import_di_table integrated_event_summary keep_sig_pairs load_example_data load_rmats overview_spicing_comparison plot_alignment_summary plot_di_volcano_dt plot_enriched_domains_counts plot_length_comparison plot_ppi_summary plot_two_transcripts_with_domains_unified probe_individual_event spliceimpact_s4_guide spliceimpact_s4_schema

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob boot broom cachem car carData cigarillo cli codetools colorspace corrplot cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray Deriv doBy dplyr farver fastmap filelock forecast formatR Formula fracdiff futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable hms httr httr2 IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr nlme nloptr nnet numDeriv openssl patchwork pbkrtest PFAM.db pillar pkgconfig png polynom prettyunits progress purrr pwalign quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas restfulr Rhtslib rjson rlang Rsamtools RSQLite rstatix rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr XML xml2 XVector yaml zoo

SpliceImpactR

Rendered fromSpliceImpactR.Rmdusingknitr::rmarkdown

Last update: 2026-03-23
Started: 2025-11-11

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

Package: SpliceImpactR 1.1.0

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

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