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GenomeInfoDb

This is thereleased version of GenomeInfoDb; for the devel version, seeGenomeInfoDb.

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

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DOI: 10.18129/B9.bioc.GenomeInfoDb


Bioconductor version: Release (3.22)

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Author: Sonali Arora [aut], Martin Morgan [aut], Marc Carlson [aut], Hervé Pagès [aut, cre], Prisca Chidimma Maduka [ctb], Atuhurira Kirabo Kakopo [ctb], Haleema Khan [ctb] (vignette translation from Sweave to Rmarkdown / HTML), Emmanuel Chigozie Elendu [ctb]

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

Citation (from within R, entercitation("GenomeInfoDb")):

Installation

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

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

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("GenomeInfoDb")
GenomeInfoDb: Introduction to GenomeInfoDbPDFR Script
Submitting your organism to GenomeInfoDbHTMLR Script
Reference ManualPDF
NEWSText
Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViewsAnnotation,DataRepresentation,Genetics,GenomeAnnotation,Software
Version1.46.2
In Bioconductor sinceBioC 2.14 (R-3.1) (11.5 years)
LicenseArtistic-2.0
DependsR (>= 4.0.0), methods,BiocGenerics(>= 0.53.2),S4Vectors(>= 0.47.6),IRanges(>= 2.41.1),Seqinfo(>= 0.99.2)
Importsstats, utils,UCSC.utils
System Requirements
URLhttps://bioconductor.org/packages/GenomeInfoDb
Bug Reportshttps://github.com/Bioconductor/GenomeInfoDb/issues
See More
SuggestsGenomeInfoDbData,R.utils,data.table,GenomicRanges,Rsamtools,GenomicAlignments,BSgenome,GenomicFeatures,TxDb.Dmelanogaster.UCSC.dm3.ensGene,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Celegans.UCSC.ce2,BSgenome.Hsapiens.NCBI.GRCh38,RUnit,BiocStyle,knitr
Linking To
Enhances
Depends On MeBSgenomeForge,CODEX,IdeoViz,SCOPE,BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38.masked,UCSCRepeatMasker,annotation,liftOver,variants
Imports MeAllelicImbalance,AnnotationHubData,ATACseqQC,atena,BaalChIP,bambu,Banksy,bedbaser,BindingSiteFinder,biovizBase,biscuiteer,breakpointR,BUSpaRse,cageminer,cardelino,cfdnakit,cfDNAPro,chimeraviz,ChIPpeakAnno,ChIPseeker,circRNAprofiler,CNEr,CNVfilteR,CNVPanelizer,CNVRanger,CopyNumberPlots,crisprDesign,CrispRVariants,Damsel,derfinder,derfinderPlot,DEScan2,diffHic,diffUTR,DMRcaller,easylift,ensembldb,EpiCompare,epimutacions,epiregulon,epivizr,EventPointer,extraChIPs,FRASER,funtooNorm,GA4GHshiny,gDNAx,GenomicDistributions,GenomicFiles,GenomicScores,ggbio,GRaNIE,GUIDEseq,Gviz,gwascat,h5vc,HiCaptuRe,HiContacts,idr2d,igblastr,karyoploteR,katdetectr,linkSet,mariner,metagene2,metaseqR2,methimpute,methodical,MethylSeekR,methylumi,missMethyl,Motif2Site,motifbreakR,multiHiCcompare,MungeSumstats,musicatk,MutationalPatterns,myvariant,NADfinder,normr,OGRE,ORFik,plotgardener,proActiv,ProteoDisco,PureCN,R3CPET,raer,RareVariantVis,RCAS,RcisTarget,recount,regioneR,regionReport,RESOLVE,rGREAT,ribosomeProfilingQC,roar,scanMiRApp,scDblFinder,scmeth,scRNAseqApp,scruff,seqCAT,SGSeq,signeR,SigsPack,Site2Target,SNPhood,SOMNiBUS,SparseSignatures,SPICEY,spiky,SpliceWiz,STADyUM,svaNUMT,svaRetro,TAPseq,TCGAutils,tidyCoverage,TnT,trackViewer,transcriptR,txdbmaker,Ularcirc,UMI4Cats,UPDhmm,VanillaICE,VariantFiltering,VariantTools,VaSP,VplotR,wiggleplotr,fitCons.UCSC.hg19,grasp2db,MafDb.1Kgenomes.phase1.GRCh38,MafDb.1Kgenomes.phase1.hs37d5,MafDb.1Kgenomes.phase3.GRCh38,MafDb.1Kgenomes.phase3.hs37d5,MafDb.ExAC.r1.0.GRCh38,MafDb.ExAC.r1.0.hs37d5,MafDb.ExAC.r1.0.nonTCGA.GRCh38,MafDb.ExAC.r1.0.nonTCGA.hs37d5,MafDb.gnomAD.r2.1.GRCh38,MafDb.gnomAD.r2.1.hs37d5,MafDb.gnomADex.r2.1.GRCh38,MafDb.gnomADex.r2.1.hs37d5,MafDb.TOPMed.freeze5.hg19,MafDb.TOPMed.freeze5.hg38,MafH5.gnomAD.v4.0.GRCh38,phastCons100way.UCSC.hg19,phastCons100way.UCSC.hg38,phastCons7way.UCSC.hg38,SNPlocs.Hsapiens.dbSNP144.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh38,SNPlocs.Hsapiens.dbSNP149.GRCh38,SNPlocs.Hsapiens.dbSNP150.GRCh38,SNPlocs.Hsapiens.dbSNP155.GRCh37,SNPlocs.Hsapiens.dbSNP155.GRCh38,XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,XtraSNPlocs.Hsapiens.dbSNP144.GRCh38,BioPlex,chipenrich.data,GenomicDistributionsData,MethylSeqData, OSTA,crispRdesignR,driveR,hicream,ICAMS,karyotapR,locuszoomr,MAAPER,Signac,tepr
Suggests MeAlphaMissenseR,AnnotationForge,AnnotationHub,annotatr,BgeeCall,BSgenome,bumphunter,Chicago,crupR,dar,DEXSeq,DFplyr,DiffBind,DMRcate,enhancerHomologSearch,epialleleR,epigraHMM,ExperimentHubData,fishpond,GA4GHclient,GENESIS,GenomicFeatures,GenomicPlot,GenomicRanges,GenomicTuples,gmapR,gmoviz,HelloRanges,HicAggR,icetea,jazzPanda,ldblock,megadepth,methrix,multicrispr,nullranges,Organism.dplyr,OUTRIDER,parglms,peakCombiner,PICB,plyinteractions,QDNAseq,RaggedExperiment,recoup,regioneReloaded,rtracklayer,scGraphVerse,scLANE,scTreeViz,Seqinfo,seqsetvis,sesame,sitadela,SomaticSignatures,splatter,SummarizedExperiment,systemPipeR,TEKRABber,treeclimbR,UCSC.utils,VariantAnnotation,BioMartGOGeneSets,CTCF,excluderanges,sesameData,xcoredata,seqpac,gkmSVM,GRIN2,polyRAD,Seurat
Links To Me
Build ReportBuild Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source PackageGenomeInfoDb_1.46.2.tar.gz
Windows Binary (x86_64) GenomeInfoDb_1.46.0.zip
macOS Binary (x86_64)GenomeInfoDb_1.46.2.tgz
macOS Binary (arm64)GenomeInfoDb_1.46.2.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/GenomeInfoDb
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/GenomeInfoDb
Bioc Package Browserhttps://code.bioconductor.org/browse/GenomeInfoDb/
Package Short Urlhttps://bioconductor.org/packages/GenomeInfoDb/
Package Downloads ReportDownload Stats
Old Source Packages for BioC 3.22Source Archive
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