BiocDuckDB
This is the development version of BiocDuckDB; to use it, please install the devel version of Bioconductor.
Bioconductor DuckDB Integration and High-Level I/O
Bioconductor version: 3.24 · Package version: 0.99.25
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.
Author: Patrick Aboyoun [aut, cre], Genentech, Inc. [cph]
Maintainer: Patrick Aboyoun <aboyounp at gene.com>
Citation
From within R, enter citation("BiocDuckDB"):
Patrick Aboyoun. BiocDuckDB: Bioconductor DuckDB Integration and High-Level I/O. doi:10.18129/B9.bioc.BiocDuckDB, R package version 0.99.25, https://bioconductor.org/packages/BiocDuckDB.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("BiocDuckDB")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 0.99.25 |
| License | MIT + file LICENSE |
| URL | https://github.com/Genentech/BiocDuckDB |
| Bug Reports | https://github.com/Genentech/BiocDuckDB/issues |
| Last updated | 2026-09-30 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| Downloads rank | 2438 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, Infrastructure, RNASeq, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/BiocDuckDB/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BiocDuckDB")| Introduction to BiocDuckDB | HTML | R Script |
| Benchmarking BiocDuckDB | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | BiocDuckDB_0.99.25.tar.gz |
| Windows binary (x86_64) | BiocDuckDB_0.99.24.zip |
| macOS binary (arm64) | BiocDuckDB_0.99.24.tgz |
| macOS binary (x86_64) | BiocDuckDB_0.99.25.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BiocDuckDB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiocDuckDB |
| Package Downloads Report | Download Stats |
Dependencies
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