Seqinfo
This is the development version of Seqinfo; for the stable release version, see Seqinfo.
A simple S4 class for storing basic information about a collection of genomic sequences
Bioconductor version: Development (3.24)
The Seqinfo class stores the names, lengths, circularity flags, and genomes for a particular collection of sequences. These sequences are typically the chromosomes and/or scaffolds of a specific genome assembly of a given organism. Seqinfo objects are rarely used as standalone objects. Instead, they are used as part of higher-level objects to represent their seqinfo() component. Examples of such higher-level objects are GRanges, RangedSummarizedExperiment, VCF, GAlignments, etc... defined in other Bioconductor infrastructure packages.
Author: Hervé Pagès [aut, cre]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("Seqinfo")):
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("Seqinfo")
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("Seqinfo")| The Seqinfo package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, DataRepresentation, GenomeAnnotation, GenomeAssembly, Infrastructure, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | Artistic-2.0 |
| Depends | methods, BiocGenerics |
| Imports | stats, S4Vectors(>= 0.47.6), IRanges |
| System Requirements | |
| URL | https://bioconductor.org/packages/Seqinfo |
| Bug Reports | https://github.com/Bioconductor/Seqinfo/issues |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Seqinfo_1.3.0.tar.gz |
| Windows Binary (x86_64) | Seqinfo_1.3.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Seqinfo_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | Seqinfo_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Seqinfo |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Seqinfo |
| Bioc Package Browser | https://code.bioconductor.org/browse/Seqinfo/ |
| Package Short Url | https://bioconductor.org/packages/Seqinfo/ |
| Package Downloads Report | Download Stats |