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: Development (3.24)
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("dbSequence")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("dbSequence")
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("dbSequence")| Data Ingestion | HTML | R Script |
| plyranges API | HTML | R Script |
| Reference Manual |
Details
| biocViews | Coverage, DataImport, DataRepresentation, Infrastructure, Sequencing, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | methods, duckdb, DBI, dbplyr, dplyr, glue, arrow, BiocIO, rtracklayer, Rsamtools, VariantAnnotation, dbProject, GenomicRanges, IRanges, rlang, cli, crayon |
| System Requirements | |
| URL | https://github.com/dbverse-org/dbSequence |
| Bug Reports | https://github.com/dbverse-org/dbSequence/issues |
See More
| Suggests | testthat (>= 3.0.0), SingleCellExperiment, scater, knitr, rmarkdown, BiocStyle, plyranges, microbenchmark |
| 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 | dbSequence_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/dbSequence/ |
| Package Short Url | https://bioconductor.org/packages/dbSequence/ |
| Package Downloads Report | Download Stats |