Package: sparrow
Type: Package
Title: Take command of set enrichment analyses through a unified
        interface
Version: 1.16.0
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 (>= 4.1.0)
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,
        KernSmooth, knitr, magrittr, matrixStats, msigdbr (>= 10.0),
        orthogene, 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
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: 7.3.2
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: make libicu-dev libpng-dev libxml2-dev libssl-dev
        perl
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:12:41 UTC
RemoteUrl: https://github.com/bioc/sparrow
RemoteRef: RELEASE_3_22
RemoteSha: fc1b95c46cde7708332e346b3a22bb2cbabea02b
NeedsCompilation: no
Packaged: 2025-11-11 17:57:12 UTC; root
Author: Steve Lianoglou [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0924-1754>),
  Arkadiusz Gladki [ctb],
  Aratus Informatics, LLC [fnd] (2023+),
  Denali Therapeutics [fnd] (2018-2022),
  Genentech [fnd] (2014 - 2017)
Maintainer: Steve Lianoglou <slianoglou@gmail.com>
Built: R 4.5.2; ; 2025-11-12 07:50:43 UTC; windows
