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DuckDBArray

DuckDB-Backed DelayedArray Implementation

Bioconductor version: 3.24 · Package version: 0.99.9

Provides DuckDB-backed implementations of DelayedArray and DelayedMatrix classes for efficient, out-of-memory operations on large array and matrix datasets. The package includes DuckDBArray, DuckDBArraySeed, and DuckDBMatrix classes with optimized matrixStats methods. Supports sparse arrays, grid partitioning, and parallel processing for scalable genomic data analysis.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DuckDBArray")

Details

MaintainerPatrick Aboyoun <aboyounp@gene.com>
AuthorPatrick Aboyoun [aut, cre], Genentech, Inc. [cph]
LicenseMIT + file LICENSE
URLhttps://github.com/Genentech/DuckDBArray
Bug Reportshttps://github.com/Genentech/DuckDBArray/issues
Downloads rank6
Source branchdevel
biocViewsDataImport, DataRepresentation, Infrastructure, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageDuckDBArray_0.99.9.tar.gz
Windows binary (x86_64)DuckDBArray_0.99.9.zip
macOS binary (arm64)DuckDBArray_0.99.9.tgz
macOS binary (x86_64)DuckDBArray_0.99.9.tgz
Dependencies

Depends: R (>= 4.5.0), methods, stats, DuckDBDataFrame, DelayedArray, SparseArray

Imports: BiocGenerics, S4Vectors, IRanges, S4Arrays, Matrix, MatrixGenerics, DBI, dplyr, dbplyr, arrow

Suggests: knitr, rmarkdown, BiocStyle, testthat, matrixStats, microbenchmark, BiocParallel, DelayedMatrixStats, ExperimentHub, HDF5Array, sparseMatrixStats, SummarizedExperiment, TileDBArray, airway

Reverse dependencies

Depends On Me (1): BiocDuckDB