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")):
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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
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) | dbSequence_0.99.1.zip |
| macOS Binary (big-sur-x86_64) | dbSequence_0.99.1.tgz |
| 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 |