DuckDBArray
This is the development version of DuckDBArray; to use it, please install the devel version of Bioconductor.
DuckDB-Backed DelayedArray Implementation
Bioconductor version: Development (3.24)
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.
Author: Patrick Aboyoun [aut, cre], Genentech, Inc. [cph]
Maintainer: Patrick Aboyoun <aboyounp at gene.com>
citation("DuckDBArray")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("DuckDBArray")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DuckDBArray")| 1. Introduction to DuckDBArray | HTML | R Script |
| 2. Benchmarking DuckDBArray | HTML | R Script |
| 3. Implementing the DuckDBArray backend | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0), methods, stats, DuckDBDataFrame, DelayedArray, SparseArray |
| Imports | BiocGenerics, S4Vectors, IRanges, S4Arrays, Matrix, MatrixGenerics, DBI, dplyr, dbplyr, arrow |
| System Requirements | |
| URL | https://github.com/Genentech/DuckDBArray |
| Bug Reports | https://github.com/Genentech/DuckDBArray/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat, matrixStats, microbenchmark, BiocParallel, DelayedMatrixStats, ExperimentHub, HDF5Array, sparseMatrixStats, SummarizedExperiment, TileDBArray, airway |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DuckDBArray_0.99.7.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | DuckDBArray_0.99.7.tgz |
| macOS Binary (sonoma-arm64) | DuckDBArray_0.99.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DuckDBArray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DuckDBArray |
| Bioc Package Browser | https://code.bioconductor.org/browse/DuckDBArray/ |
| Package Short Url | https://bioconductor.org/packages/DuckDBArray/ |
| Package Downloads Report | Download Stats |