BiocDuckDB/DESCRIPTION at main · Genentech/BiocDuckDB · GitHub

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Package: BiocDuckDB
Version: 0.99.11
Date: 2026-07-28
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
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 (>= 4.6.0),
    methods,
    stats,
    DuckDBDataFrame,
    DuckDBArray,
    DuckDBGRanges
Imports:
    BiocGenerics,
    BiocParallel,
    S4Vectors,
    IRanges,
    GenomicRanges,
    SparseArray,
    DelayedArray,
    MatrixGenerics,
    SummarizedExperiment,
    SingleCellExperiment,
    MultiAssayExperiment,
    MultiAssaySpatialExperiment,
    metapod,
    scran,
    scuttle,
    DBI,
    dplyr,
    dbplyr,
    duckdb,
    arrow,
    jsonlite
Suggests:
    knitr,
    rmarkdown,
    BiocStyle,
    testthat,
    jsonvalidate,
    grDevices,
    Matrix,
    matrixStats,
    nanoparquet,
    png,
    sf,
    sfarrow,
    SpatialExperiment,
    DuckDBSpatial,
    ExperimentHub,
    HDF5Array,
    ZarrArray,
    scater,
    airway,
    scRNAseq
biocViews:
    DataImport,
    DataRepresentation,
    Infrastructure,
    RNASeq,
    Sequencing,
    SingleCell,
    Software
VignetteBuilder: knitr
Encoding: UTF-8
Collate:
    'MultiAssaySpatialExperiments-internals.R'
    'DuckDBDataFrame-spatial.R'
    'DuckDBDualSubset-class.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'
    'readParquet.R'
    'writeDatapackage.R'
    'writeParquet.R'
    'writeStreamingResource.R'
Config/roxygen2/version: 8.0.0