DuckDBGRanges
This is the development version of DuckDBGRanges; to use it, please install the devel version of Bioconductor.
DuckDB-Backed GenomicRanges Implementation
Bioconductor version: Development (3.24)
Provides DuckDB-backed implementations of GenomicRanges data structures for efficient, out-of-memory operations on large genomic interval datasets. The package includes DuckDBGRanges and DuckDBGRangesList classes with optimized range operations including restrict, flank, shift, findOverlaps, and distance calculations. Ideal for variant analysis, scATAC-seq peak analysis, and other genomic workflows requiring memory-efficient range operations on large datasets.
Author: Patrick Aboyoun [aut, cre], Genentech, Inc. [cph]
Maintainer: Patrick Aboyoun <aboyounp at gene.com>
citation("DuckDBGRanges")):
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("DuckDBGRanges")
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("DuckDBGRanges")| 1. Introduction to DuckDBGRanges | HTML | R Script |
| 2. Benchmarking DuckDBGRanges | HTML | R Script |
| 3. Design and extension of DuckDBGRanges | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Sequencing, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0), methods, stats, DuckDBDataFrame, GenomicRanges |
| Imports | bit64, BiocGenerics, S4Vectors, IRanges, Seqinfo, DelayedArray, DBI, dplyr, dbplyr |
| System Requirements | |
| URL | https://github.com/Genentech/DuckDBGRanges |
| Bug Reports | https://github.com/Genentech/DuckDBGRanges/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat, microbenchmark, arrow, TxDb.Hsapiens.UCSC.hg38.knownGene |
| 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 | DuckDBGRanges_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | DuckDBGRanges_0.99.4.tgz |
| macOS Binary (sonoma-arm64) | DuckDBGRanges_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DuckDBGRanges |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DuckDBGRanges |
| Bioc Package Browser | https://code.bioconductor.org/browse/DuckDBGRanges/ |
| Package Short Url | https://bioconductor.org/packages/DuckDBGRanges/ |
| Package Downloads Report | Download Stats |