Seqinfo

This is the released version of Seqinfo; for the devel version, see Seqinfo.

All versions

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

Bioconductor version: Release (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] ORCID: 0009-0002-8272-4522

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

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

Hervé Pagès. Seqinfo: A simple S4 class for storing basic information about a collection of genomic sequences. doi:10.18129/B9.bioc.Seqinfo, R package version 1.2.0, https://bioconductor.org/packages/Seqinfo.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

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
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataRepresentation, GenomeAnnotation, GenomeAssembly, Infrastructure, Software
Version	1.2.0
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

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, BSgenome, BSgenomeForge, bumphunter, CSAR, extraChIPs, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, OrganismDbi, Rsamtools, txdbmaker, VariantAnnotation
Imports Me	alabaster.ranges, amplican, annoLinker, AnnotationHubData, annotatr, ATACseqTFEA, atena, ballgown, BasicSTARRseq, Bioc.gff, biovizBase, BiSeq, bnbc, branchpointer, bsseq, CAGEfightR, CAGEr, casper, cBioPortalData, CexoR, chipenrich, ChIPexoQual, chromVAR, cleanUpdTSeq, CleanUpRNAseq, cn.mops, CNEr, Cogito, compEpiTools, consensusSeekeR, conumee, crisprBowtie, crisprBwa, crisprDesign, CRISPRseek, crisprShiny, crisprViz, crupR, csaw, DAMEfinder, DaMiRseq, decompTumor2Sig, DegCre, demuxSNP, derfinder, derfinderPlot, DEScan2, DEWSeq, dmGsea, DMRcaller, DMRcate, DMRScan, dmrseq, DominoEffect, easyRNASeq, ELMER, enhancerHomologSearch, ensembldb, EpiCompare, epigraHMM, EpiMix, EpiTxDb, epivizrData, epivizrStandalone, esATAC, FindIT2, FLAMES, G4SNVHunter, GA4GHclient, GA4GHshiny, gcapc, gDNAx, geneAttribution, genomation, GenomAutomorphism, genomeIntervals, GenomicCoordinates, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicPlot, GenomicScores, GenomicState, GenVisR, geomeTriD, ggbio, gmoviz, goseq, GOTHiC, grasp2db, GreyListChIP, Gviz, gwascat, heatmaps, HicAggR, HiCBricks, HiCDOC, HiCExperiment, HiCParser, hicVennDiagram, HiTC, IMAS, InPAS, INSPEcT, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, ldblock, maser, metaseqR2, methInheritSim, methylKit, methylPipe, methylSig, minfi, MinimumDistance, monaLisa, mosaics, motifmatchr, MotifPeeker, motifTestR, MouseFM, msgbsR, multicrispr, MutationalPatterns, MutSeqR, myvariant, NoRCE, nucleR, nullranges, OGRE, OMICsPCA, Organism.dplyr, panelcn.mops, peakCombiner, periodicDNA, PICB, pipeFrame, plyinteractions, plyranges, podkat, pram, prebs, ProteoDisco, PureCN, QDNAseq, qpgraph, qsea, QuasR, r3Cseq, raer, RaggedExperiment, ramr, rCGH, recoup, regioneR, regionReport, REMP, rfPred, RgnTX, RiboCrypt, RiboProfiling, riboSeqR, ribosomeProfilingQC, rigvf, RJMCMCNucleosomes, rnaEditr, RNAmodR, RTCGAToolbox, rtracklayer, scanMiR, scmeth, segmentSeq, SeqArray, seqsetvis, sesame, sesameData, sevenC, SGSeq, ShortRead, sitadela, soGGi, SomaticSignatures, spatzie, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, SummarizedExperiment, svaNUMT, svaRetro, tadar, TCGAutils, TENxIO, TEQC, TFBSTools, trackViewer, transmogR, tRNAscanImport, TVTB, tximeta, VariantFiltering, VplotR, YAPSA
Suggests Me	AlphaMissenseR, AnnotationHub, RAIDS, RNAmodR.AlkAnilineSeq, RNAmodR.RiboMethSeq, splicelogic, TFEA.ChIP, TFutils
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Seqinfo_1.2.0.tar.gz
Windows Binary (x86_64)	Seqinfo_1.2.0.zip
macOS Binary (big-sur-x86_64)	Seqinfo_1.2.0.tgz
macOS Binary (sonoma-arm64)	Seqinfo_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Seqinfo
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Seqinfo
Package Short Url	https://bioconductor.org/packages/Seqinfo/
Package Downloads Report	Download Stats