Package: OutSplice
Type: Package
Title: Comparison of Splicing Events between Tumor and Normal Samples
Version: 1.10.0
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-release.r-universe.dev
Date/Publication: 2025-10-29 15:23:03 UTC
RemoteUrl: https://github.com/bioc/OutSplice
RemoteRef: RELEASE_3_22
RemoteSha: 394473e74d52b2b8b6e921f157366b15b9197674
NeedsCompilation: no
Packaged: 2025-11-20 07:32:14 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>
Built: R 4.5.2; ; 2025-11-20 07:35:35 UTC; windows
