Registration Open for GBCC2025:
Joint Galaxy/Bioconductor Conference!

Seqinfo

This is the development version of Seqinfo; to use it, please install the devel version of Bioconductor.

A simple S4 class for storing basic information about a collection of genomic sequences


Bioconductor version: Development (3.22)

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] ORCID iD ORCID: 0009-0002-8272-4522

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("Seqinfo")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF

Details

biocViews Annotation, DataRepresentation, GenomeAnnotation, GenomeAssembly, Infrastructure, Software
Version 0.99.0
In Bioconductor since BioC 3.22 (R-4.5)
License Artistic-2.0
Depends methods, BiocGenerics
Imports stats, S4Vectors, IRanges
System Requirements
URL https://bioconductor.org/packages/Seqinfo
Bug Reports https://github.com/Bioconductor/Seqinfo/issues
See More
Suggests GenomeInfoDb, GenomicRanges, BSgenome, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Celegans.UCSC.ce2, RUnit, knitr, rmarkdown, BiocStyle
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 Seqinfo_0.99.0.tar.gz
Windows Binary (x86_64) Seqinfo_0.99.0.zip
macOS Binary (x86_64) Seqinfo_0.99.0.tgz
macOS Binary (arm64) Seqinfo_0.99.0.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