Package: BiocDuckDB
Version: 0.99.28
Date: 2026-10-21
Title: Bioconductor DuckDB Integration and High-Level I/O
Description: Integration package providing high-level Parquet I/O
        functions and optimized methods for single-cell analysis
        workflows using DuckDB-backed data structures. Includes
        readParquet and writeParquet functions for seamless
        serialization of SummarizedExperiment, SingleCellExperiment,
        MultiAssayExperiment, and MultiAssaySpatialExperiment objects,
        plus SQL-optimized implementations of scran and scuttle methods
        for variance modeling, marker detection, QC metrics, and
        normalization. This package brings together DuckDBDataFrame,
        DuckDBArray, DuckDBGRanges, and DuckDBSpatial (optional) for
        complete Bioconductor integration.
Authors@R: 
    c(
        person("Patrick", "Aboyoun", role=c("aut", "cre"), email="aboyounp@gene.com"),
        person("Genentech, Inc.", role="cph")
    )
License: MIT + file LICENSE
URL: https://github.com/Genentech/BiocDuckDB
BugReports: https://github.com/Genentech/BiocDuckDB/issues
Copyright: See the file inst/COPYRIGHTS for third-party schema
        components bundled in inst/schema/ (Frictionless Data Package
        specifications, in the public domain under The Unlicense).
Depends: R (>= 4.5.0), methods, stats, DuckDBDataFrame, DuckDBArray,
        DuckDBGRanges
Imports: BiocGenerics, BiocParallel, Matrix, S4Vectors, IRanges,
        GenomicRanges, SparseArray, DelayedArray, MatrixGenerics,
        SummarizedExperiment, SingleCellExperiment,
        MultiAssayExperiment, MultiAssaySpatialExperiment, metapod,
        beachmat, BiocSingular, scran, scuttle, DBI, dplyr, dbplyr,
        duckdb, arrow, jsonlite
Suggests: knitr, rmarkdown, BiocStyle, testthat, jsonvalidate,
        grDevices, matrixStats, nanoparquet, png, sf, sfarrow,
        S4Arrays, SpatialExperiment, DuckDBSpatial, ExperimentHub,
        HDF5Array, ZarrArray, irlba, scater, airway, scRNAseq
biocViews: DataImport, DataRepresentation, Infrastructure, RNASeq,
        Sequencing, SingleCell, Software
VignetteBuilder: knitr
Encoding: UTF-8
Collate: 'BiocDuckDB-package.R'
        'MultiAssaySpatialExperiments-internals.R'
        'DuckDBDataFrame-spatial.R' 'DuckDBDualSubset-class.R'
        'initializeOptions.R' 'initializeCpp.R' 'DuckDBIrlbaParam.R'
        'DuckDBMatrix-scran.R' 'DuckDBMatrix-scuttle.R'
        'MultiAssaySpatialExperiment-query.R'
        'MultiAssaySpatialExperiment-spatial.R'
        'SingleCellExperiments-internals.R'
        'SingleCellExperiment-colTables.R'
        'SingleCellExperiment-loadings.R'
        'SingleCellExperiment-pairs.R'
        'SingleCellExperiment-rowTables.R' 'fieldtypes.R'
        'loadIntoMemory.R' 'readParquet.R' 'writeDatapackage.R'
        'writeParquet.R' 'writeStreamingResource.R'
Config/roxygen2/version: 8.1.1
Config/pak/sysreqs: libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev
        libglpk-dev libmagick++-dev gsfonts libicu-dev libxml2-dev
        libssl-dev libproj-dev libsqlite3-dev libudunits2-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-21 16:13:30 UTC
RemoteUrl: https://github.com/bioc/BiocDuckDB
RemoteRef: HEAD
RemoteSha: d0fbd4601dda6a4709c728fd51d78989c59ceaf0
NeedsCompilation: no
Packaged: 2026-10-21 21:04:38 UTC; root
Author: Patrick Aboyoun [aut, cre],
  Genentech, Inc. [cph]
Maintainer: Patrick Aboyoun <aboyounp@gene.com>