Package: SpliceImpactR
Type: Package
Title: An R package to identify functional impacts due to alternative
        RNA processing events
Version: 1.0.0
Authors@R: c(person(given="Zachary", family="Wakefield",
    email = "zachpw@bu.edu",
    role = c("cre", "aut"),
    comment = c(ORCID = "0000-0002-9104-0934")),
    person(given="Ana", family="Fiszbein",
    email = "anafisz@bu.edu",
    role = c("aut")))
Description: 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.
License: GPL-3
Encoding: UTF-8
Imports: data.table, BiocFileCache, BiocParallel, Biostrings,
        GenomicRanges, SummarizedExperiment, biomaRt, IRanges, PFAM.db,
        dplyr, ggplot2, ggpubr, patchwork, pwalign, rtracklayer,
        scales, stats, tidyr, tools, utils, magrittr, methods,
        S4Vectors
RoxygenNote: 7.3.3
biocViews: AlternativeSplicing, DifferentialSplicing,
        StatisticalMethod, Alignment
Suggests: devtools, testthat (>= 3.0.0), knitr, rmarkdown, cowplot,
        stringr, readr, tibble, BiocStyle, clusterProfiler,
        AnnotationDbi, msigdbr, org.Hs.eg.db, org.Mm.eg.db
VignetteBuilder: knitr
Config/testthat/edition: 3
BugReports: https://github.com/fiszbein-lab/SpliceImpactR/issues
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:06:51 UTC
RemoteUrl: https://github.com/bioc/SpliceImpactR
RemoteRef: RELEASE_3_23
RemoteSha: c3b74ba3e43a73357f1b3b84e8e40d7a1c3144c8
NeedsCompilation: no
Packaged: 2026-04-30 06:40:13 UTC; root
Author: Zachary Wakefield [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-9104-0934>),
  Ana Fiszbein [aut]
Maintainer: Zachary Wakefield <zachpw@bu.edu>
Depends: R (>= 3.5.0)
Built: R 4.6.0; ; 2026-04-30 07:51:49 UTC; unix
