Package: OutSplice
Type: Package
Title: Comparison of Splicing Events between Tumor and Normal Samples
Version: 1.13.0
Authors@R: c(person("Joseph", "Bendik", role = "aut", comment = c(ORCID = "0000-0003-0877-5639")),
    person("Sandhya", "Kalavacherla", role = "aut", comment = c(ORCID = "0000-0003-0485-9042")),
    person("Michael", "Considine", role = "aut", comment = c(ORCID = "0000-0002-8666-4857")), 
    person("Bahman", "Afsari", role = "aut", comment = c(ORCID = "0000-0001-8717-7199")),
    person("Michael F.", "Ochs", role = "aut"), 
    person("Joseph", "Califano", role = "aut", comment = c(ORCID = "0000-0002-4715-6761")), 
    person("Daria A.", "Gaykalova", role = "aut", comment = c(ORCID = "0000-0001-5037-0147")), 
    person("Elana", "Fertig", role = "aut", comment = c(ORCID = "0000-0003-3204-342X")), 
    person("Theresa", "Guo", email = "twguo@health.ucsd.edu", role = c("cre", "aut"), comment = c(ORCID = "0000-0002-1689-3275")))
Description: An easy to use tool that can compare splicing events in
        tumor and normal tissue samples using either a user generated
        matrix, or data from The Cancer Genome Atlas (TCGA). This
        package generates a matrix of splicing outliers that are
        significantly over or underexpressed in tumors samples compared
        to normal denoted by chromosome location. The package also will
        calculate the splicing burden in each tumor and characterize
        the types of splicing events that occur.
Encoding: UTF-8
License: GPL-2
Depends: R(>= 4.3)
Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0),
        GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db
        (>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2),
        TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>=
        0.36.0)
Suggests: BiocStyle, knitr, rmarkdown, testthat
VignetteBuilder: knitr
biocViews: AlternativeSplicing, DifferentialExpression,
        DifferentialSplicing, GeneExpression, RNASeq, Software,
        VariantAnnotation
BugReports: https://github.com/GuoLabUCSD/OutSplice/issues
URL: https://github.com/GuoLabUCSD/OutSplice
RoxygenNote: 7.2.3
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:00:42 UTC
RemoteUrl: https://github.com/bioc/OutSplice
RemoteRef: HEAD
RemoteSha: 60d4ae860a4acd09106f01d4df4cc4a2da7459c0
NeedsCompilation: no
Packaged: 2026-07-04 23:26:18 UTC; root
Author: Joseph Bendik [aut] (ORCID: <https://orcid.org/0000-0003-0877-5639>),
  Sandhya Kalavacherla [aut] (ORCID:
    <https://orcid.org/0000-0003-0485-9042>),
  Michael Considine [aut] (ORCID:
    <https://orcid.org/0000-0002-8666-4857>),
  Bahman Afsari [aut] (ORCID: <https://orcid.org/0000-0001-8717-7199>),
  Michael F. Ochs [aut],
  Joseph Califano [aut] (ORCID: <https://orcid.org/0000-0002-4715-6761>),
  Daria A. Gaykalova [aut] (ORCID:
    <https://orcid.org/0000-0001-5037-0147>),
  Elana Fertig [aut] (ORCID: <https://orcid.org/0000-0003-3204-342X>),
  Theresa Guo [cre, aut] (ORCID: <https://orcid.org/0000-0002-1689-3275>)
Maintainer: Theresa Guo <twguo@health.ucsd.edu>