dbSequence
This is the development version of dbSequence; to use it, please install the devel version of Bioconductor.
DuckDB-Backed Interface for Large-Scale Genomic Data
Bioconductor version: 3.24 · Package version: 0.99.1
Provides a DuckDB-backed infrastructure for working with large-scale genomic data that exceeds available memory. Supports lazy evaluation of genomic ranges and efficient overlap queries. Integrates with Bioconductor classes (GRanges, BiocIO) and provides plyranges-compatible API.
Author: Edward C. Ruiz [aut, cre] 
, Ruben Dries [rev], National Human Genome Research Institute [fnd] (grant: 1R01HG014487-01)
Maintainer: Edward C. Ruiz <ecr7407 at gmail.com>
Citation
From within R, enter citation("dbSequence"):
Edward C. Ruiz. dbSequence: DuckDB-Backed Interface for Large-Scale Genomic Data. doi:10.18129/B9.bioc.dbSequence, R package version 0.99.1, https://bioconductor.org/packages/dbSequence.
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("dbSequence")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 0.99.1 |
| License | MIT + file LICENSE |
| URL | https://github.com/dbverse-org/dbSequence |
| Bug Reports | https://github.com/dbverse-org/dbSequence/issues |
| Last updated | 2026-06-30 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| Downloads rank | 2401 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, DataImport, DataRepresentation, Infrastructure, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/dbSequence/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dbSequence")| Data Ingestion | HTML | R Script |
| plyranges API | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | dbSequence_0.99.1.tar.gz |
| Windows binary (x86_64) | dbSequence_0.99.1.zip |
| macOS binary (arm64) | dbSequence_0.99.1.tgz |
| macOS binary (x86_64) | dbSequence_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dbSequence |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dbSequence |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: methods, duckdb, DBI, dbplyr, dplyr, glue, arrow, BiocIO, rtracklayer, Rsamtools, VariantAnnotation, dbProject, GenomicRanges, IRanges, rlang, cli, crayon
Suggests: testthat (>= 3.0.0), SingleCellExperiment, scater, knitr, rmarkdown, BiocStyle, plyranges, microbenchmark