dbSequence
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dbSequence")Details
| Maintainer | Edward C. Ruiz <ecr7407@gmail.com> |
| Author | Edward C. Ruiz [aut, cre] (ORCID: <https://orcid.org/0000-0002-9174-5387>), Ruben Dries [rev], National Human Genome Research Institute [fnd] (grant: 1R01HG014487-01) |
| License | MIT + file LICENSE |
| URL | https://github.com/dbverse-org/dbSequence |
| Bug Reports | https://github.com/dbverse-org/dbSequence/issues |
| Downloads rank | 44 |
| Source branch | devel |
| biocViews | Coverage, DataImport, DataRepresentation, Infrastructure, Sequencing, Software |
Documentation
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 |
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