DESCRIPTION

Package: sparrow
Type: Package
Title: Take command of set enrichment analyses through a unified interface
Version: 1.11.0
Authors@R: c(
    person(
        "Steve", "Lianoglou", role = c("aut", "cre"),
        email = "slianoglou@gmail.com",
        comment = c(ORCID = "0000-0002-0924-1754")),
    person(
        "Arkadiusz", "Gladki", role = c("ctb"),
        email = "gladki.arkadiusz@gmail.com"),
    person("Aratus Informatics, LLC", role = c("fnd"), comment = "2023+"),
    person("Denali Therapeutics", role = c("fnd"), comment = "2018-2022"),
    person("Genentech", role = c("fnd"), comment = "2014 - 2017"))
Description: Provides a unified interface to a variety of GSEA techniques from
    different bioconductor packages. Results are harmonized into a single object
    and can be interrogated uniformly for quick exploration and interpretation
    of results. Interactive exploration of GSEA results is enabled through
    a shiny app provided by a sparrow.shiny sibling package.
URL: https://github.com/lianos/sparrow
BugReports: https://github.com/lianos/sparrow/issues
Depends:
    R (>= 4.0)
Imports:
    babelgene (>= 21.4),
    BiocGenerics,
    BiocParallel,
    BiocSet,
    checkmate,
    circlize,
    ComplexHeatmap (>= 2.0),
    data.table (>= 1.10.4),
    DelayedMatrixStats,
    edgeR (>= 3.18.1),
    ggplot2 (>= 2.2.0),
    graphics,
    grDevices,
    GSEABase,
    irlba,
    limma,
    Matrix,
    methods,
    plotly (>= 4.9.0),
    stats,
    utils,
    viridis
Suggests:
    AnnotationDbi,
    BiasedUrn,
    Biobase (>= 2.24.0),
    BiocStyle,
    DESeq2,
    dplyr,
    dtplyr,
    fgsea,
    GSVA,
    GO.db,
    goseq,
    hexbin,
    magrittr,
    matrixStats,
    msigdbr (>= 7.4.1),
    KernSmooth,
    knitr,
    PANTHER.db (>= 1.0.3),
    R.utils,
    reactome.db,
    rmarkdown,
    SummarizedExperiment,
    statmod,
    stringr,
    testthat,
    webshot
biocViews: GeneSetEnrichment, Pathways
BiocType: Software
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Collate:
    'AllClasses.R'
    'AllGenerics.R'
    'GeneSetDb-class.R'
    'GeneSetDb-methods.R'
    'SparrowResult-methods.R'
    'aaa.R'
    'bioc-accessors.R'
    'calculateIndividualLogFC.R'
    'convertIdentifiers.R'
    'validateInputs.R'
    'do.camera.R'
    'do.cameraPR.R'
    'do.fgsea.R'
    'do.fry.R'
    'do.geneSetTest.R'
    'do.goseq.R'
    'do.logFC.R'
    'do.ora.R'
    'do.roast.R'
    'do.romer.R'
    'do.svdGeneSetTest.R'
    'geneSetSummaryByGenes.R'
    'get-kegg.R'
    'get-msigdb.R'
    'get-panther.R'
    'get-reactome.R'
    'gsea-helpers.R'
    'package.R'
    'plots-corplot.R'
    'plots-interactive.R'
    'plots-mgheatmap.R'
    'plots-mgheatmap2.R'
    'renameCollections.R'
    'renameRows.R'
    'scale_rows.R'
    'scoreSingleSamples.R'
    'seas.R'
    'single-sample-scoring-methods.R'
    'species.R'
    'testing-helpers.R'
    'utilities.R'
    'volcano_plot.R'
    'zzz.R'
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)