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: Development (3.24)
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("BiocDuckDB")):
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("BiocDuckDB")
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("BiocDuckDB")| 1. Introduction to BiocDuckDB | HTML | R Script |
| 2. Benchmarking BiocDuckDB | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, RNASeq, Sequencing, SingleCell, Software |
| Version | 0.99.22 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://github.com/Genentech/BiocDuckDB |
| Bug Reports | https://github.com/Genentech/BiocDuckDB/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat, jsonvalidate, grDevices, Matrix, matrixStats, nanoparquet, png, sf, sfarrow, S4Arrays, SpatialExperiment, DuckDBSpatial, ExperimentHub, HDF5Array, ZarrArray, scater, airway, scRNAseq |
| 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 | BiocDuckDB_0.99.22.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | BiocDuckDB_0.99.22.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/BiocDuckDB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiocDuckDB |
| Bioc Package Browser | https://code.bioconductor.org/browse/BiocDuckDB/ |
| Package Short Url | https://bioconductor.org/packages/BiocDuckDB/ |
| Package Downloads Report | Download Stats |