Movatterモバイル変換

[0]ホーム
URL:

Bioconductor 3.22 Released

Bioconductor home
Menu

Seqinfo

This is thereleased version of Seqinfo; for the devel version, seeSeqinfo.

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

Platform availability badgeRanking badgeSupport activity badgeYears in BioConductor badgeBuild results badgeLast commit badgeDependency count badge

DOI: 10.18129/B9.bioc.Seqinfo


Bioconductor version: Release (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, entercitation("Seqinfo")):

Installation

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

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

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Seqinfo")
The Seqinfo packageHTMLR Script
Reference ManualPDF
NEWSText

Need some help? Ask on the Bioconductor Support site!

Details

biocViewsAnnotation,DataRepresentation,GenomeAnnotation,GenomeAssembly,Infrastructure,Software
Version1.0.0
In Bioconductor sinceBioC 3.22 (R-4.5) (< 6 months)
LicenseArtistic-2.0
Dependsmethods,BiocGenerics
Importsstats,S4Vectors(>= 0.47.6),IRanges
System Requirements
URLhttps://bioconductor.org/packages/Seqinfo
Bug Reportshttps://github.com/Bioconductor/Seqinfo/issues
See More
SuggestsGenomeInfoDb,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 MeBiostrings,BSgenome,BSgenomeForge,bumphunter,CSAR,extraChIPs,GenomeInfoDb,GenomicAlignments,GenomicFeatures,GenomicRanges,GenomicTuples,gmapR,groHMM,HelloRanges,OrganismDbi,Rsamtools,txdbmaker,VariantAnnotation
Imports Mealabaster.ranges,amplican,AnnotationHubData,annotatr,ATACseqTFEA,atena,ballgown,Bioc.gff,biovizBase,BiSeq,bnbc,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,decompTumor2Sig,DegCre,demuxSNP,derfinder,derfinderPlot,DEScan2,DEWSeq,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,GenomicFiles,GenomicInteractionNodes,GenomicInteractions,GenomicOZone,GenomicPlot,GenomicScores,geomeTriD,ggbio,gmoviz,goseq,GOTHiC,GreyListChIP,Gviz,gwascat,heatmaps,HicAggR,HiCBricks,HiCDOC,HiCExperiment,HiCParser,hicVennDiagram,HiTC,InPAS,INSPEcT,InteractionSet,IsoformSwitchAnalyzeR,IVAS,karyoploteR,ldblock,maser,metaseqR2,methInheritSim,methylKit,methylPipe,methylSig,minfi,MinimumDistance,mobileRNA,monaLisa,mosaics,motifmatchr,MotifPeeker,motifTestR,MouseFM,msgbsR,multicrispr,MutationalPatterns,myvariant,nearBynding,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,recoup,regioneR,regionReport,REMP,rfPred,RgnTX,RiboCrypt,RiboProfiling,riboSeqR,ribosomeProfilingQC,rigvf,RJMCMCNucleosomes,rnaEditr,RNAmodR,RTCGAToolbox,rtracklayer,scanMiR,scmeth,segmentSeq,SeqArray,seqsetvis,sesame,sevenC,SGSeq,ShortRead,SingleMoleculeFootprinting,sitadela,SomaticSignatures,SplicingGraphs,SPLINTER,srnadiff,strandCheckR,SummarizedExperiment,svaNUMT,svaRetro,tadar,TCGAutils,TEKRABber,TENxIO,TEQC,TFBSTools,trackViewer,transmogR,tRNAscanImport,TVTB,tximeta,VariantFiltering,VplotR,YAPSA,GenomicState,grasp2db,sesameData
Suggests MeAlphaMissenseR,AnnotationHub,RAIDS,RNAmodR.AlkAnilineSeq,RNAmodR.RiboMethSeq,TFEA.ChIP,TFutils
Links To Me
Build ReportBuild Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source PackageSeqinfo_1.0.0.tar.gz
Windows Binary (x86_64) Seqinfo_1.0.0.zip (64-bit only)
macOS Binary (x86_64)Seqinfo_1.0.0.tgz
macOS Binary (arm64)Seqinfo_1.0.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/Seqinfo
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/Seqinfo
Bioc Package Browserhttps://code.bioconductor.org/browse/Seqinfo/
Package Short Urlhttps://bioconductor.org/packages/Seqinfo/
Package Downloads ReportDownload Stats
[8]ページ先頭
©2009-2025 Movatter.jp