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 (3.23)
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")):
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("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 | 1.1.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| 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
| 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 | Biostrings, CSAR, GenomeInfoDb, GenomicAlignments, GenomicRanges, GenomicTuples, Rsamtools |
| Imports Me | alabaster.ranges, Bioc.gff, bnbc, cn.mops, csaw, DEWSeq, DMRScan, easyRNASeq, GenomAutomorphism, genomeIntervals, GenomicScores, heatmaps, HiCBricks, HiCDOC, HiCExperiment, HiCParser, InteractionSet, ldblock, MinimumDistance, mosaics, motifTestR, MouseFM, nucleR, panelcn.mops, peakCombiner, PICB, prebs, QDNAseq, RaggedExperiment, ramr, rfPred, riboSeqR, rigvf, scanMiR, segmentSeq, sesame, ShortRead, strandCheckR, SummarizedExperiment, TENxIO, TEQC, VplotR, GenomicState, grasp2db, sesameData |
| Suggests Me | AlphaMissenseR, AnnotationHub |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Seqinfo_1.1.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |