{
  "_id": "6a1af36d1d7bb097a09f83f7",
  "Package": "sparrow",
  "Type": "Package",
  "Title": "Take command of set enrichment analyses through a unified\ninterface",
  "Version": "1.19.0",
  "Authors@R": "c(\nperson(\n\"Steve\", \"Lianoglou\", role = c(\"aut\", \"cre\"),\nemail = \"slianoglou@gmail.com\",\ncomment = c(ORCID = \"0000-0002-0924-1754\")),\nperson(\n\"Arkadiusz\", \"Gladki\", role = c(\"ctb\"),\nemail = \"gladki.arkadiusz@gmail.com\"),\nperson(\"Aratus Informatics, LLC\", role = c(\"fnd\"), comment = \"2023+\"),\nperson(\"Denali Therapeutics\", role = c(\"fnd\"), comment = \"2018-2022\"),\nperson(\"Genentech\", role = c(\"fnd\"), comment = \"2014 - 2017\"))",
  "Description": "Provides a unified interface to a variety of GSEA\ntechniques from different bioconductor packages. Results are\nharmonized into a single object and can be interrogated\nuniformly for quick exploration and interpretation of results.\nInteractive exploration of GSEA results is enabled through a\nshiny app provided by a sparrow.shiny sibling package.",
  "URL": "https://github.com/lianos/sparrow",
  "BugReports": "https://github.com/lianos/sparrow/issues",
  "biocViews": "GeneSetEnrichment, Pathways",
  "BiocType": "Software",
  "VignetteBuilder": "knitr",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Collate": "'AllClasses.R' 'AllGenerics.R' 'GeneSetDb-class.R'\n'GeneSetDb-methods.R' 'SparrowResult-methods.R' 'aaa.R'\n'bioc-accessors.R' 'calculateIndividualLogFC.R'\n'convertIdentifiers.R' 'validateInputs.R' 'do.camera.R'\n'do.cameraPR.R' 'do.fgsea.R' 'do.fry.R' 'do.geneSetTest.R'\n'do.goseq.R' 'do.logFC.R' 'do.ora.R' 'do.roast.R' 'do.romer.R'\n'do.svdGeneSetTest.R' 'geneSetSummaryByGenes.R' 'get-kegg.R'\n'get-msigdb.R' 'get-panther.R' 'get-reactome.R'\n'gsea-helpers.R' 'package.R' 'plots-corplot.R'\n'plots-interactive.R' 'plots-mgheatmap.R' 'plots-mgheatmap2.R'\n'renameCollections.R' 'renameRows.R' 'scale_rows.R'\n'scoreSingleSamples.R' 'seas.R'\n'single-sample-scoring-methods.R' 'species.R'\n'testing-helpers.R' 'utilities.R' 'volcano_plot.R' 'zzz.R'",
  "RoxygenNote": "7.3.2",
  "Roxygen": "list(markdown = TRUE)",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev perl zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:07 UTC",
  "RemoteUrl": "https://github.com/bioc/sparrow",
  "RemoteRef": "HEAD",
  "RemoteSha": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:44:13 UTC",
    "User": "root"
  },
  "Author": "Steve Lianoglou [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-0924-1754>),\nArkadiusz Gladki [ctb],\nAratus Informatics, LLC [fnd] (2023+),\nDenali Therapeutics [fnd] (2018-2022),\nGenentech [fnd] (2014 - 2017)",
  "Maintainer": "Steve Lianoglou <slianoglou@gmail.com>",
  "MD5sum": "f7d476ebc6c1f81db63db646b6646b20",
  "_user": "bioc",
  "_type": "src",
  "_file": "sparrow_1.19.0.tar.gz",
  "_fileid": "989d74652c1f5027c3188f71f769a92475842a9cf73e0e56d1f00936f510cf9b",
  "_filesize": 4525185,
  "_sha256": "989d74652c1f5027c3188f71f769a92475842a9cf73e0e56d1f00936f510cf9b",
  "_created": "2026-05-30T09:44:13.000Z",
  "_published": "2026-05-30T14:25:49.568Z",
  "_jobs": [
    {
      "job": 78640492650,
      "time": 349,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307463439"
    },
    {
      "job": 78640492642,
      "time": 608,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307486164"
    },
    {
      "job": 78640492639,
      "time": 685,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307490523"
    },
    {
      "job": 78640492646,
      "time": 366,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308848159"
    },
    {
      "job": 78640492644,
      "time": 406,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308851721"
    },
    {
      "job": 78639640598,
      "time": 515,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307274626"
    },
    {
      "job": 78640492640,
      "time": 327,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307459616"
    },
    {
      "job": 78640492658,
      "time": 833,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307504695"
    },
    {
      "job": 78640492645,
      "time": 749,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307498031"
    },
    {
      "job": 78640492643,
      "time": 753,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307497252"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/sparrow",
  "_commit": {
    "id": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381027
  },
  "_maintainer": {
    "name": "Steve Lianoglou",
    "email": "slianoglou@gmail.com",
    "login": "lianos",
    "twitter": "@_lianos_",
    "description": "Closing the gap between computational- and bench- scientists // #rstats oR bust!",
    "uuid": 25496,
    "orcid": "0000-0002-0924-1754"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "babelgene",
      "version": ">= 21.4",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "BiocSet",
      "role": "Imports"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "version": ">= 2.0",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.10.4",
      "role": "Imports"
    },
    {
      "package": "DelayedMatrixStats",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "version": ">= 3.18.1",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.2.0",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "GSEABase",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "version": ">= 4.9.0",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "viridis",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "BiasedUrn",
      "role": "Suggests"
    },
    {
      "package": "Biobase",
      "version": ">= 2.24.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "DESeq2",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "dtplyr",
      "role": "Suggests"
    },
    {
      "package": "fgsea",
      "role": "Suggests"
    },
    {
      "package": "GSVA",
      "role": "Suggests"
    },
    {
      "package": "GO.db",
      "role": "Suggests"
    },
    {
      "package": "goseq",
      "role": "Suggests"
    },
    {
      "package": "hexbin",
      "role": "Suggests"
    },
    {
      "package": "KernSmooth",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "magrittr",
      "role": "Suggests"
    },
    {
      "package": "matrixStats",
      "role": "Suggests"
    },
    {
      "package": "msigdbr",
      "version": ">= 10.0",
      "role": "Suggests"
    },
    {
      "package": "orthogene",
      "role": "Suggests"
    },
    {
      "package": "PANTHER.db",
      "version": ">= 1.0.3",
      "role": "Suggests"
    },
    {
      "package": "R.utils",
      "role": "Suggests"
    },
    {
      "package": "reactome.db",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "statmod",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "webshot",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.19.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.18.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genesetenrichment",
    "pathways",
    "bioinformatics",
    "gsea"
  ],
  "_stars": 23,
  "_contributors": [
    {
      "user": "lianos",
      "count": 64,
      "uuid": 25496
    },
    {
      "user": "jwokaty",
      "count": 12,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "gladkia",
      "count": 2,
      "uuid": 41166437
    },
    {
      "user": "tomsing1",
      "count": 1,
      "uuid": 10490984
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 670,
    "source": "https://www.bioconductor.org/packages/stats/bioc/sparrow"
  },
  "_devurl": "https://github.com/lianos/sparrow",
  "_searchresults": 19,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/sparrow.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/lianos/sparrow",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addCollectionMetadata",
    "addGeneSetMetadata",
    "annotateGeneSetMembership",
    "calculateIndividualLogFC",
    "collectionMetadata",
    "combine",
    "conform",
    "convertIdentifiers",
    "corplot",
    "eigenWeightedMean",
    "encode_gskey",
    "exampleBiocSet",
    "exampleDgeResult",
    "exampleExpressionSet",
    "exampleGeneSetDb",
    "exampleGeneSetDF",
    "exampleGeneSets",
    "exampleSparrowResult",
    "failWith",
    "featureIdMap",
    "featureIds",
    "featureIdType",
    "featureIdType<-",
    "geneSet",
    "geneSetCollectionURLfunction",
    "geneSetCollectionURLfunction<-",
    "geneSetDb",
    "GeneSetDb",
    "geneSets",
    "geneSetsStats",
    "geneSetSummaryByGenes",
    "geneSetURL",
    "getKeggCollection",
    "getKeggGeneSetDb",
    "getMSigCollection",
    "getMSigGeneSetDb",
    "getPantherCollection",
    "getPantherGeneSetDb",
    "getReactomeCollection",
    "goseq",
    "gsdScore",
    "hasGeneSet",
    "hasGeneSetCollection",
    "incidenceMatrix",
    "iplot",
    "is.active",
    "is.conformed",
    "logFC",
    "mgheatmap",
    "mgheatmap2",
    "msg",
    "nrow",
    "ora",
    "p.matrix",
    "plot_ora_bias",
    "randomGeneSetDb",
    "renameCollections",
    "renameRows",
    "result",
    "resultNames",
    "results",
    "scale_rows",
    "scoreSingleSamples",
    "seas",
    "sparrow_methods",
    "species_info",
    "split_gskey",
    "subsetByFeatures",
    "tabulateResults",
    "unconform",
    "validateInputs",
    "volcanoPlot",
    "volcanoStatsTable",
    "zScore"
  ],
  "_help": [
    {
      "page": "sub-GeneSetDb-ANY-ANY-ANY-method",
      "title": "Subset whole genesets from a GeneSetDb",
      "topics": [
        "[,GeneSetDb,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "addGeneSetMetadata",
      "title": "Add metadata at the geneset level.",
      "topics": [
        "addGeneSetMetadata"
      ]
    },
    {
      "page": "all.equal.GeneSetDb",
      "title": "Checks equality (feature parity) between GeneSetDb objects",
      "topics": [
        "all.equal.GeneSetDb"
      ]
    },
    {
      "page": "annotateGeneSetMembership",
      "title": "Annotates rows of a data.frame with geneset membership from a GeneSetDb",
      "topics": [
        "annotateGeneSetMembership"
      ]
    },
    {
      "page": "calculateIndividualLogFC",
      "title": "Utility function to run limma differential expression analysis",
      "topics": [
        "calculateIndividualLogFC"
      ]
    },
    {
      "page": "collectionMetadata",
      "title": "Gene Set Collection Metadata",
      "topics": [
        "addCollectionMetadata",
        "collectionMetadata",
        "collectionMetadata,GeneSetDb,character,character-method",
        "collectionMetadata,GeneSetDb,character,missing-method",
        "collectionMetadata,GeneSetDb,missing,missing-method",
        "featureIdType",
        "featureIdType,GeneSetDb-method",
        "featureIdType<-",
        "featureIdType<-,GeneSetDb-method",
        "geneSetURL",
        "geneSetURL,GeneSetDb-method",
        "geneSetURL,SparrowResult-method"
      ]
    },
    {
      "page": "combine-GeneSetDb-GeneSetDb-method",
      "title": "Combines two GeneSetDb objects together",
      "topics": [
        "combine,GeneSetDb,GeneSetDb-method"
      ]
    },
    {
      "page": "combine-SparrowResult-SparrowResult-method",
      "title": "Combines two SparrowResult objects together.",
      "topics": [
        "combine,SparrowResult,SparrowResult-method"
      ]
    },
    {
      "page": "conform",
      "title": "(Re)-map geneset IDs to the rows in an expression object.",
      "topics": [
        "conform",
        "conform,GeneSetDb-method",
        "is.conformed",
        "unconform",
        "unconform,GeneSetDb-method"
      ]
    },
    {
      "page": "conversion",
      "title": "Convert a GeneSetDb to other formats.",
      "topics": [
        "as.data.frame",
        "as.data.frame.GeneSetDb",
        "as.data.table",
        "as.data.table.GeneSetDb",
        "as.list",
        "conversion"
      ]
    },
    {
      "page": "convertIdentifiers",
      "title": "Converts internal feature identifiers in a GeneSetDb to a set of new ones.",
      "topics": [
        "convertIdentifiers",
        "convertIdentifiers,BiocSet-method",
        "convertIdentifiers,GeneSetDb-method"
      ]
    },
    {
      "page": "corplot",
      "title": "Plots the correlation among the columns of a numeric matrix.",
      "topics": [
        "corplot"
      ]
    },
    {
      "page": "eigenWeightedMean",
      "title": "Single sample gene set score by a weighted average of the genes in geneset",
      "topics": [
        "eigenWeightedMean"
      ]
    },
    {
      "page": "gskey",
      "title": "Converts collection,name combination to key for geneset",
      "topics": [
        "encode_gskey",
        "split_gskey"
      ]
    },
    {
      "page": "examples",
      "title": "Functions that load data for use in examples and testing.",
      "topics": [
        "exampleBiocSet",
        "exampleDgeResult",
        "exampleExpressionSet",
        "exampleGeneSetDb",
        "exampleGeneSetDF",
        "exampleGeneSets",
        "exampleSparrowResult"
      ]
    },
    {
      "page": "failWith",
      "title": "Utility function to try and fail with grace.",
      "topics": [
        "failWith"
      ]
    },
    {
      "page": "featureIdMap",
      "title": "Fetch the featureIdMap for a 'GeneSetDb'",
      "topics": [
        "featureIdMap",
        "featureIdMap,GeneSetDb-method"
      ]
    },
    {
      "page": "featureIds",
      "title": "Returns the relevant featureIds for a given geneset.",
      "topics": [
        "featureIds",
        "featureIds,GeneSetDb-method",
        "featureIds,SparrowResult-method"
      ]
    },
    {
      "page": "geneSet",
      "title": "Fetches information for a gene set",
      "topics": [
        "geneSet",
        "geneSet,GeneSetDb-method",
        "geneSet,SparrowResult-method"
      ]
    },
    {
      "page": "geneSetCollectionURLfunction",
      "title": "Get/set the gene set collection url function for a geneset collection",
      "topics": [
        "geneSetCollectionURLfunction",
        "geneSetCollectionURLfunction,GeneSetDb-method",
        "geneSetCollectionURLfunction,SparrowResult-method",
        "geneSetCollectionURLfunction<-",
        "geneSetCollectionURLfunction<-,GeneSetDb-method"
      ]
    },
    {
      "page": "SparrowResult-utilities",
      "title": "Fetches the GeneSetDb from SparrowResult",
      "topics": [
        "geneSetDb"
      ]
    },
    {
      "page": "GeneSetDb-class",
      "title": "A container for geneset definitions.",
      "topics": [
        ".GeneSetDb",
        "GeneSetDb",
        "GeneSetDb-class"
      ]
    },
    {
      "page": "geneSets",
      "title": "Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult",
      "topics": [
        "geneSets",
        "geneSets,GeneSetDb-method",
        "geneSets,SparrowResult-method",
        "length,GeneSetDb-method",
        "nrow,GeneSetDb-method"
      ]
    },
    {
      "page": "geneSetsStats",
      "title": "Summarizes useful statistics per gene set from a SparrowResult",
      "topics": [
        "geneSetsStats"
      ]
    },
    {
      "page": "geneSetSummaryByGenes",
      "title": "Summarize geneset:feature relationships for specified set of features",
      "topics": [
        "geneSetSummaryByGenes",
        "geneSetSummaryByGenes,GeneSetDb-method",
        "geneSetSummaryByGenes,SparrowResult-method"
      ]
    },
    {
      "page": "getKeggCollection",
      "title": "Retrieves the KEGG gene set collection via its REST API",
      "topics": [
        "getKeggCollection",
        "getKeggGeneSetDb"
      ]
    },
    {
      "page": "getMSigCollection",
      "title": "Fetches gene set collections from the moleular signature database (MSigDB)",
      "topics": [
        "getMSigCollection",
        "getMSigGeneSetDb"
      ]
    },
    {
      "page": "getPantherCollection",
      "title": "Get pathways/GOslim collections from PANTHER.db Biocondcutor package.",
      "topics": [
        "getPantherCollection",
        "getPantherGeneSetDb"
      ]
    },
    {
      "page": "getReactomeCollection",
      "title": "Retrieve gene set collections from from reactome.db",
      "topics": [
        "getReactomeCollection",
        "getReactomeGeneSetDb"
      ]
    },
    {
      "page": "goseq",
      "title": "Perform goseq Enrichment tests across a GeneSetDb.",
      "topics": [
        "goseq"
      ]
    },
    {
      "page": "gsdScore",
      "title": "Single sample geneset score using SVD based eigengene value per sample.",
      "topics": [
        "gsdScore"
      ]
    },
    {
      "page": "hasGeneSet",
      "title": "Check to see if the GeneSetDb has a collection,name GeneSet defined",
      "topics": [
        "hasGeneSet"
      ]
    },
    {
      "page": "hasGeneSetCollection",
      "title": "Check if a collection exists in the 'GeneSetDb'",
      "topics": [
        "hasGeneSetCollection"
      ]
    },
    {
      "page": "incidenceMatrix",
      "title": "Creates a 1/0 matrix to indicate geneset membership to target object.",
      "topics": [
        "incidenceMatrix"
      ]
    },
    {
      "page": "iplot",
      "title": "Visualize gene level behavior of genes within a geneset across a contrast.",
      "topics": [
        "iplot"
      ]
    },
    {
      "page": "is.active",
      "title": "Interrogate \"active\" status of a given geneset.",
      "topics": [
        "is.active"
      ]
    },
    {
      "page": "logFC",
      "title": "Extract the individual fold changes statistics for elements in the expression object.",
      "topics": [
        "logFC"
      ]
    },
    {
      "page": "mgheatmap",
      "title": "Creates a \"geneset smart\" ComplexHeatmap::Heatmap",
      "topics": [
        "mgheatmap"
      ]
    },
    {
      "page": "mgheatmap2",
      "title": "Creates a \"geneset smart\" ComplexHeatmap::Heatmap",
      "topics": [
        "mgheatmap2"
      ]
    },
    {
      "page": "msg",
      "title": "Utility function to cat a message to stderr (by default)",
      "topics": [
        "msg"
      ]
    },
    {
      "page": "ora",
      "title": "Performs an overrepresentation analysis, (optionally) accounting for bias.",
      "topics": [
        "ora",
        "plot_ora_bias"
      ]
    },
    {
      "page": "p.matrix",
      "title": "Assembles a matrix of nominal or adjusted pvalues from a sparrow::seas result",
      "topics": [
        "p.matrix"
      ]
    },
    {
      "page": "randomGeneSetDb",
      "title": "Generates a fake GeneSetDb by sampling from features in a seas input.",
      "topics": [
        "randomGeneSetDb"
      ]
    },
    {
      "page": "renameCollections",
      "title": "Rename the collections in a GeneSetDb",
      "topics": [
        "renameCollections"
      ]
    },
    {
      "page": "renameRows",
      "title": "Smartly/easily rename the rows of an object.",
      "topics": [
        "renameRows"
      ]
    },
    {
      "page": "results",
      "title": "Interrogate the results of a sparrow::seas analysis stored in a SparrowResult",
      "topics": [
        "result",
        "result.SparrowResult",
        "resultNames",
        "results",
        "tabulateResults"
      ]
    },
    {
      "page": "scale_rows",
      "title": "Centers and scales the rows of a numeric matrix.",
      "topics": [
        "scale_rows"
      ]
    },
    {
      "page": "scoreSingleSamples",
      "title": "Generates single sample gene set scores across a datasets by many methods",
      "topics": [
        "scoreSingleSamples"
      ]
    },
    {
      "page": "seas",
      "title": "Performs a plethora of set enrichment analyses over varied inputs.",
      "topics": [
        "seas"
      ]
    },
    {
      "page": "sparrow_methods",
      "title": "Lists the supported GSEA methods by sparrow",
      "topics": [
        "sparrow_methods"
      ]
    },
    {
      "page": "SparrowResult",
      "title": "A SparrowResult object holds the results from a sparrow::seas() call.",
      "topics": [
        ".SparrowResult",
        "SparrowResult",
        "SparrowResult-class"
      ]
    },
    {
      "page": "species_info",
      "title": "Match a species query to the regularized species info.",
      "topics": [
        "species_info"
      ]
    },
    {
      "page": "ssGSEA.normalize",
      "title": "Normalize a vector of ssGSEA scores in the ssGSEA way.",
      "topics": [
        "ssGSEA.normalize"
      ]
    },
    {
      "page": "subset.GeneSetDb",
      "title": "Subset GeneSetDb to only include specified genesets.",
      "topics": [
        "subset.GeneSetDb"
      ]
    },
    {
      "page": "subsetByFeatures",
      "title": "Subset a GeneSetDb to only include geneSets with specified features.",
      "topics": [
        "subsetByFeatures",
        "subsetByFeatures,GeneSetDb-method"
      ]
    },
    {
      "page": "validateInputs",
      "title": "Validate the input objects to a GSEA call.",
      "topics": [
        "validateInputs"
      ]
    },
    {
      "page": "volcanoPlot",
      "title": "Create an interactive volcano plot",
      "topics": [
        "volcanoPlot"
      ]
    },
    {
      "page": "volcanoStatsTable",
      "title": "Extracts x and y axis values from objects to create input for volcano plot",
      "topics": [
        "volcanoStatsTable"
      ]
    },
    {
      "page": "zScore",
      "title": "Calculate single sample geneset score by average z-score method",
      "topics": [
        "zScore"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/sparrow/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "babelgene",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "BiocSet",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "checkmate",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "doParallel",
    "dplyr",
    "edgeR",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GetoptLong",
    "ggplot2",
    "GlobalOptions",
    "glue",
    "graph",
    "gridExtra",
    "GSEABase",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "ontologyIndex",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shape",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "sparrow.Rmd",
      "filename": "sparrow.html",
      "title": "Performing gene set enrichment analyses with sparrow",
      "author": "Steve Lianoglou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Standard Workflow",
        "Data Setup",
        "Data Analysis",
        "Differential Gene Expression",
        "Gene Set Enrichment Analysis",
        "Gene Sets to Test",
        "Running sparrow",
        "Implicit Differential Expression",
        "Explicit GSEA",
        "Exploring Results",
        "Plotting",
        "Interactive Exploration",
        "Singe Sample Gene Set Scoring",
        "Generating Single Sample Gene Set Scores",
        "Visualizing Single Sample Gene Set Scores",
        "Gene Set Based Heatmap with mgheatmap",
        "Gene level based heatmap (from genesets)",
        "Gene set-based heatmap",
        "The GeneSetDb Class",
        "Building a GeneSetDb",
        "Subsetting a GeneSetDb",
        "Active vs Inactive Gene Sets",
        "Accessing members of a gene set",
        "Mapping of gene set featureIds to target expression containers",
        "Customizing Analyses",
        "Custom Differential Expression",
        "Custom GSEA",
        "Reproducibility"
      ],
      "created": "2021-05-04 13:40:30",
      "modified": "2025-04-01 20:07:26",
      "commits": 13
    }
  ],
  "_score": 6.242541428298384,
  "_indexed": true,
  "_nocasepkg": "sparrow",
  "_universes": [
    "bioc",
    "lianos"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-05-30T10:17:27.000Z",
      "distro": "noble",
      "commit": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
      "fileid": "f853bbb787ed2bab8297c270a80aa9c09b962c2d729970da045820d2005f57c3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-05-30T10:17:35.000Z",
      "distro": "noble",
      "commit": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
      "fileid": "819263f5b47755cde9a8439741bee51a5b9cd010b1c346b9b0a34553235844c0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-05-30T14:21:08.000Z",
      "commit": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
      "fileid": "31b42a9c1ae96c0c619ba0991181773ca0b66b87cffd96001e228480e7c06611",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-05-30T14:21:43.000Z",
      "commit": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
      "fileid": "b522f520d39b2c4cf49b0e5bedcdd8be450b47ccdbd1dc57452178a090283819",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.19.0",
      "date": "2026-05-30T10:17:32.000Z",
      "commit": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
      "fileid": "a5cff2aea2ffb8f6cdf8ca27aa3c8ecbb2ec4583dbceb306d803b09ec0fd2f65",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-05-30T10:17:08.000Z",
      "commit": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
      "fileid": "858a5126ebb1adcf3ed7e16e32b7924e7203e479fb9b66e2548a6a2426275c5b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-05-30T10:16:47.000Z",
      "commit": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
      "fileid": "1b2318ca0351721d9fc6c851b9671668cca5b6f3675a64decc68de4812e010d8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-05-30T10:16:46.000Z",
      "commit": "e66d9ccddd1ae1e6e2a20fbaef49b361fb7c4028",
      "fileid": "6139dcf20fa7cebc99957d539f29eee8ae08f668ef3bd99fc683466728bff422",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676251722"
    }
  ]
}