{
  "_id": "6a62000b35834fefe99ec22c",
  "Package": "BiocDuckDB",
  "Version": "0.99.5",
  "Date": "2026-07-22",
  "Title": "Bioconductor DuckDB Integration and High-Level I/O",
  "Description": "Integration package providing high-level Parquet I/O\nfunctions and optimized methods for single-cell analysis\nworkflows using DuckDB-backed data structures. Includes\nreadParquet and writeParquet functions for seamless\nserialization of SummarizedExperiment, SingleCellExperiment,\nMultiAssayExperiment, and MultiAssaySpatialExperiment objects,\nplus SQL-optimized implementations of scran and scuttle methods\nfor variance modeling, marker detection, QC metrics, and\nnormalization. This package brings together DuckDBDataFrame,\nDuckDBArray, DuckDBGRanges, and DuckDBSpatial (optional) for\ncomplete Bioconductor integration.",
  "Authors@R": "c(\nperson(\"Patrick\", \"Aboyoun\", role=c(\"aut\", \"cre\"), email=\"aboyounp@gene.com\"),\nperson(\"Genentech, Inc.\", role=\"cph\")\n)",
  "License": "MIT + file LICENSE",
  "Copyright": "See the file inst/COPYRIGHTS for third-party schema\ncomponents bundled in inst/schema/ (Frictionless Data Package\nspecifications, in the public domain under The Unlicense).",
  "biocViews": "DataImport, DataRepresentation, Infrastructure, RNASeq,\nSequencing, SingleCell, Software",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Collate": "'MultiAssaySpatialExperiments-internals.R'\n'DuckDBDataFrame-spatial.R' 'DuckDBDualSubset-class.R'\n'DuckDBMatrix-scran.R' 'DuckDBMatrix-scuttle.R'\n'MultiAssaySpatialExperiment-query.R'\n'MultiAssaySpatialExperiment-spatial.R'\n'SingleCellExperiments-internals.R'\n'SingleCellExperiment-colTables.R'\n'SingleCellExperiment-loadings.R'\n'SingleCellExperiment-pairs.R'\n'SingleCellExperiment-rowTables.R' 'fieldtypes.R'\n'readParquet.R' 'writeDatapackage.R' 'writeParquet.R'",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev libmagick++-dev gsfonts libicu-dev libxml2-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev xz-utils\nzlib1g-dev",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-07-23 04:24:26 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/BiocDuckDB",
  "RemoteRef": "HEAD",
  "RemoteSha": "17137e0acaf3455f364399d1989149d6d3117396",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-23 11:32:38 UTC",
    "User": "root"
  },
  "Author": "Patrick Aboyoun [aut, cre],\nGenentech, Inc. [cph]",
  "Maintainer": "Patrick Aboyoun <aboyounp@gene.com>",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "BiocDuckDB_0.99.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/053cb136c4ab7bbb53e6e346ba3dd093884d01045d1debb81a6bf5711c8d66db",
  "_filesize": 481390,
  "_sha256": "053cb136c4ab7bbb53e6e346ba3dd093884d01045d1debb81a6bf5711c8d66db",
  "_expires": "2026-10-31T11:50:33.000Z",
  "_created": "2026-07-23T11:32:38.000Z",
  "_published": "2026-07-23T11:50:35.268Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 10
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30003060148",
  "_status": "success",
  "_upstream": "https://github.com/BiocStaging/BiocDuckDB",
  "_commit": {
    "id": "17137e0acaf3455f364399d1989149d6d3117396",
    "author": "Patrick Aboyoun <aboyoun.patrick@gene.com>",
    "committer": "Patrick Aboyoun <aboyoun.patrick@gene.com>",
    "message": "test: add cross-path append is schema-consistent test\n",
    "time": 1784780666
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  "_maintainer": {
    "name": "Patrick Aboyoun",
    "email": "aboyounp@gene.com"
  },
  "_distro": "resolute",
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      "version": ">= 4.5.0",
      "role": "Depends"
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      "package": "methods",
      "role": "Depends"
    },
    {
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  "_owner": "biocstaging",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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  "_tags": [],
  "_topics": [
    "dataimport",
    "datarepresentation",
    "infrastructure",
    "rnaseq",
    "sequencing",
    "singlecell",
    "software"
  ],
  "_stars": 0,
  "_contributors": [
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      "count": 68,
      "uuid": 171627243
    }
  ],
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    "type": "organization",
    "name": "BiocStaging",
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  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BiocDuckDB"
  },
  "_devurl": "https://github.com/biocstaging/biocduckdb",
  "_rbuild": "4.6.1",
  "_assets": [
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    "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",
    "LICENSE",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "annotateWithRegions",
    "calculateAverage",
    "calculateCPM",
    "calculateTPM",
    "colPair<-",
    "colPairs<-",
    "colTable",
    "colTable<-",
    "colTableNames",
    "colTableNames<-",
    "colTables",
    "colTables<-",
    "correlatePairs",
    "findMarkers",
    "geometricSizeFactors",
    "librarySizeFactors",
    "linkSpatialMap",
    "modelGeneCV2",
    "modelGeneVar",
    "modelGeneVarByPoisson",
    "normalizeCounts",
    "numDetectedAcrossFeatures",
    "pairwiseBinom",
    "pairwiseTTests",
    "perCellQCMetrics",
    "perFeatureQCMetrics",
    "readGeoParquetForMASE",
    "readParquet",
    "readParquetForMASE",
    "rowLoading",
    "rowLoading<-",
    "rowLoadingNames",
    "rowLoadingNames<-",
    "rowLoadings",
    "rowLoadings<-",
    "rowPair<-",
    "rowPairs<-",
    "rowTable",
    "rowTable<-",
    "rowTableNames",
    "rowTableNames<-",
    "rowTables",
    "rowTables<-",
    "scoreMarkers",
    "spatialCoordinateSystems",
    "spatialElementJoin",
    "spatialJoin",
    "spatialMatch",
    "spatialOverlaps",
    "spatialViews",
    "subsetByBoundingBox",
    "subsetByPolygon",
    "sumCountsAcrossFeatures",
    "summarizeAssayByGroup",
    "summaryMarkerStats",
    "validateSpatialMap",
    "writeDatapackage",
    "writeParquet"
  ],
  "_help": [
    {
      "page": "DuckDBDataFrame-spatial",
      "title": "DuckDBDataFrame spatial methods",
      "topics": [
        "DuckDBDataFrame-spatial",
        "spatialJoin,DuckDBDataFrame,DuckDBDataFrame-method",
        "spatialMatch,DuckDBDataFrame,DataFrame-method",
        "spatialMatch,DuckDBDataFrame,DuckDBDataFrame-method",
        "spatialOverlaps,DuckDBDataFrame-method"
      ]
    },
    {
      "page": "DuckDBDualSubset-class",
      "title": "DuckDBDualSubset objects",
      "topics": [
        "c,DuckDBDualSubset-method",
        "DuckDBDualSubset-class",
        "length,DuckDBDualSubset-method",
        "[,DuckDBDualSubset,ANY,ANY,ANY-method",
        "[<-,DuckDBDualSubset,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "DuckDBMatrix-scran",
      "title": "DuckDBMatrix scran methods",
      "topics": [
        "correlatePairs,DuckDBMatrix-method",
        "DuckDBMatrix-scran",
        "findMarkers,DuckDBMatrix-method",
        "modelGeneCV2,DuckDBMatrix-method",
        "modelGeneVar,DuckDBMatrix-method",
        "modelGeneVarByPoisson,DuckDBMatrix-method",
        "pairwiseBinom,DuckDBMatrix-method",
        "pairwiseTTests,DuckDBMatrix-method",
        "scoreMarkers,DuckDBMatrix-method",
        "summaryMarkerStats,DuckDBMatrix-method"
      ]
    },
    {
      "page": "DuckDBMatrix-scuttle",
      "title": "DuckDBMatrix scuttle methods",
      "topics": [
        "calculateAverage,DuckDBMatrix-method",
        "calculateCPM,DuckDBMatrix-method",
        "calculateTPM,DuckDBMatrix-method",
        "DuckDBMatrix-scuttle",
        "geometricSizeFactors,DuckDBMatrix-method",
        "librarySizeFactors,DuckDBMatrix-method",
        "normalizeCounts,DuckDBMatrix-method",
        "numDetectedAcrossFeatures,DuckDBMatrix-method",
        "perCellQCMetrics,DuckDBMatrix-method",
        "perFeatureQCMetrics,DuckDBMatrix-method",
        "sumCountsAcrossFeatures,DuckDBMatrix-method",
        "summarizeAssayByGroup,DuckDBMatrix-method"
      ]
    },
    {
      "page": "linkSpatialMap",
      "title": "Link assay observations to their spatial layer rows",
      "topics": [
        "linkSpatialMap"
      ]
    },
    {
      "page": "MultiAssaySpatialExperiment-spatial",
      "title": "MultiAssaySpatialExperiment lazy spatial methods",
      "topics": [
        "annotateWithRegions,MultiAssaySpatialExperiment-method",
        "MultiAssaySpatialExperiment-spatial",
        "readGeoParquetForMASE,character-method",
        "readParquetForMASE,character-method",
        "subsetByBoundingBox,MultiAssaySpatialExperiment-method",
        "subsetByPolygon,MultiAssaySpatialExperiment-method"
      ]
    },
    {
      "page": "readParquet",
      "title": "Read Parquet Representation of a Bioconductor Object",
      "topics": [
        "readParquet"
      ]
    },
    {
      "page": "SingleCellExperiment-colTables",
      "title": "Sample table methods",
      "topics": [
        "colTable",
        "colTable,SingleCellExperiment,character-method",
        "colTable,SingleCellExperiment,missing-method",
        "colTable,SingleCellExperiment,numeric-method",
        "colTable<-",
        "colTable<-,SingleCellExperiment,character-method",
        "colTable<-,SingleCellExperiment,missing-method",
        "colTable<-,SingleCellExperiment,numeric-method",
        "colTableNames",
        "colTableNames,SingleCellExperiment-method",
        "colTableNames<-",
        "colTableNames<-,SingleCellExperiment,character-method",
        "colTables",
        "colTables,SingleCellExperiment-method",
        "colTables<-",
        "colTables<-,SingleCellExperiment-method",
        "SingleCellExperiment-colTables"
      ]
    },
    {
      "page": "SingleCellExperiment-loadings",
      "title": "Feature loading methods",
      "topics": [
        "rowLoading",
        "rowLoading,SingleCellExperiment,character-method",
        "rowLoading,SingleCellExperiment,missing-method",
        "rowLoading,SingleCellExperiment,numeric-method",
        "rowLoading<-",
        "rowLoading<-,SingleCellExperiment,character-method",
        "rowLoading<-,SingleCellExperiment,missing-method",
        "rowLoading<-,SingleCellExperiment,numeric-method",
        "rowLoadingNames",
        "rowLoadingNames,SingleCellExperiment-method",
        "rowLoadingNames<-",
        "rowLoadingNames<-,SingleCellExperiment,character-method",
        "rowLoadings",
        "rowLoadings,SingleCellExperiment-method",
        "rowLoadings<-",
        "rowLoadings<-,SingleCellExperiment-method",
        "SingleCellExperiment-loadings"
      ]
    },
    {
      "page": "SingleCellExperiment-pairs",
      "title": "colPairs/rowPairs setters for DuckDBSelfHits",
      "topics": [
        "colPair<-,SingleCellExperiment,character,DuckDBSelfHits-method",
        "colPair<-,SingleCellExperiment,missing,DuckDBSelfHits-method",
        "colPair<-,SingleCellExperiment,numeric,DuckDBSelfHits-method",
        "colPairs<-,SingleCellExperiment,DuckDBSelfHits-method",
        "rowPair<-,SingleCellExperiment,character,DuckDBSelfHits-method",
        "rowPair<-,SingleCellExperiment,missing,DuckDBSelfHits-method",
        "rowPair<-,SingleCellExperiment,numeric,DuckDBSelfHits-method",
        "rowPairs<-,SingleCellExperiment,DuckDBSelfHits-method",
        "SingleCellExperiment-pairs"
      ]
    },
    {
      "page": "SingleCellExperiment-rowTables",
      "title": "Feature table methods",
      "topics": [
        "rowTable",
        "rowTable,SingleCellExperiment,character-method",
        "rowTable,SingleCellExperiment,missing-method",
        "rowTable,SingleCellExperiment,numeric-method",
        "rowTable<-",
        "rowTable<-,SingleCellExperiment,character-method",
        "rowTable<-,SingleCellExperiment,missing-method",
        "rowTable<-,SingleCellExperiment,numeric-method",
        "rowTableNames",
        "rowTableNames,SingleCellExperiment-method",
        "rowTableNames<-",
        "rowTableNames<-,SingleCellExperiment,character-method",
        "rowTables",
        "rowTables,SingleCellExperiment-method",
        "rowTables<-",
        "rowTables<-,SingleCellExperiment-method",
        "SingleCellExperiment-rowTables"
      ]
    },
    {
      "page": "spatialCoordinateSystems",
      "title": "Coordinate systems of a MultiAssaySpatialExperiment",
      "topics": [
        "spatialCoordinateSystems"
      ]
    },
    {
      "page": "spatialElementJoin",
      "title": "Spatial join between two elements of a MASE",
      "topics": [
        "spatialElementJoin"
      ]
    },
    {
      "page": "spatialViews",
      "title": "On-the-fly DuckDB views over a MASE's spatial elements",
      "topics": [
        "spatialViews"
      ]
    },
    {
      "page": "validateSpatialMap",
      "title": "Validate a MASE's spatialMap referential integrity",
      "topics": [
        "validateSpatialMap"
      ]
    },
    {
      "page": "writeDatapackage",
      "title": "Write a Frictionless datapackage.json envelope",
      "topics": [
        "writeDatapackage"
      ]
    },
    {
      "page": "writeParquet",
      "title": "Write Parquet Representation of a Bioconductor Object",
      "topics": [
        "writeParquet",
        "writeParquet,ANY-method",
        "writeParquet,Assays-method",
        "writeParquet,data.frame-method",
        "writeParquet,DataFrame-method",
        "writeParquet,DuckDBDataFrame-method",
        "writeParquet,DuckDBGRanges-method",
        "writeParquet,DuckDBGRangesList-method",
        "writeParquet,DuckDBSelfHits-method",
        "writeParquet,DuckDBTable-method",
        "writeParquet,DuckDBTransposedDataFrame-method",
        "writeParquet,ExperimentList-method",
        "writeParquet,GenomicRanges-method",
        "writeParquet,GenomicRangesList-method",
        "writeParquet,List-method",
        "writeParquet,list-method",
        "writeParquet,MultiAssayExperiment-method",
        "writeParquet,MultiAssaySpatialExperiment-method",
        "writeParquet,PointsLayerList-method",
        "writeParquet,SelfHits-method",
        "writeParquet,ShapesLayerList-method",
        "writeParquet,SingleCellExperiment-method",
        "writeParquet,SummarizedExperiment-method",
        "writeParquet,TransposedDataFrame-method"
      ]
    }
  ],
  "_readme": "https://github.com/BiocStaging/BiocDuckDB/raw/HEAD/README.md",
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    "arrow",
    "askpass",
    "assertthat",
    "assorthead",
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    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
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