GenomeInfoDb

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see GenomeInfoDb.

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

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("GenomeInfoDb")

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("GenomeInfoDb")

GenomeInfoDb: Introduction to GenomeInfoDb	PDF	R Script
GenomeInfoDb: Submitting your organism to GenomeInfoDb	PDF	R Script
Reference Manual	PDF
NEWS	Text
Simple tasks genomeInfoDb	Video

Details

biocViews	Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version	1.30.1
In Bioconductor since	BioC 2.14 (R-3.1) (10 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.25.12), IRanges(>= 2.13.12)
Imports	stats, stats4, utils, RCurl, GenomeInfoDbData
System Requirements
URL	https://bioconductor.org/packages/GenomeInfoDb
Bug Reports	https://github.com/Bioconductor/GenomeInfoDb/issues

See More

Suggests	GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr
Linking To
Enhances
Depends On Me	Biostrings, BRGenomics, BSgenome, bumphunter, ChIPComp, CODEX, CSAR, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, IdeoViz, Rsamtools, SCOPE, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, VariantAnnotation, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me	AllelicImbalance, alpine, amplican, AneuFinder, AnnotationHubData, annotatr, ASpediaFI, ATACseqQC, atena, BaalChIP, ballgown, bambu, BasicSTARRseq, biovizBase, biscuiteer, BiSeq, bnbc, branchpointer, breakpointR, BSgenome, bsseq, BUSpaRse, CAGEfightR, cageminer, CAGEr, casper, cBioPortalData, CexoR, chimeraviz, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPpeakAnno, ChIPseeker, chromstaR, chromVAR, CINdex, circRNAprofiler, cleanUpdTSeq, cn.mops, CNEr, CNVfilteR, CNVPanelizer, CNVRanger, Cogito, compEpiTools, consensusSeekeR, conumee, CopyNumberPlots, CopywriteR, CRISPRseek, CrispRVariants, csaw, customProDB, DAMEfinder, dasper, decompTumor2Sig, DeepBlueR, derfinder, derfinderPlot, DEScan2, DEWSeq, diffHic, diffloop, diffUTR, DMRcate, DMRScan, dmrseq, DominoEffect, easyRNASeq, ELMER, ENCODExplorer, enhancerHomologSearch, enrichTF, ensembldb, ensemblVEP, epialleleR, epigenomix, epigraHMM, EpiTxDb, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomeCopy, exomePeak2, FindIT2, fitCons.UCSC.hg19, FRASER, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, GenoGAM, genomation, genomeIntervals, GenomicDistributions, GenomicDistributionsData, GenomicFiles, GenomicInteractions, GenomicOZone, GenomicScores, GenomicState, genotypeeval, GenVisR, ggbio, gmoviz, GOTHiC, grasp2db, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCBricks, HiCDCPlus, HiTC, HTSeqGenie, idr2d, IMAS, InPAS, INSPEcT, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, ldblock, MACPET, MADSEQ, 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.v3.1.1.GRCh38, maser, metagene, metagene2, metaseqR2, metavizr, MethCP, methimpute, methInheritSim, methylKit, methylPipe, MethylSeqData, methylSig, methylumi, minfi, MinimumDistance, MMAPPR2, monaLisa, mosaics, motifbreakR, motifmatchr, MouseFM, msgbsR, multicrispr, multiHiCcompare, MungeSumstats, musicatk, MutationalPatterns, myvariant, NADfinder, nearBynding, netDx, normr, nucleR, nullranges, NxtIRFcore, ODER, OMICsPCA, ORFik, Organism.dplyr, panelcn.mops, periodicDNA, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, pipeFrame, plyranges, podkat, pram, prebs, proActiv, profileplyr, ProteoDisco, ProteomicsAnnotationHubData, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, RaggedExperiment, RareVariantVis, Rcade, RCAS, rCGH, RcisTarget, recount, recoup, regioneR, regionReport, REMP, Repitools, RiboCrypt, RiboProfiling, riboSeqR, ribosomeProfilingQC, RJMCMCNucleosomes, RLSeq, rnaEditr, RNAmodR, roar, RTCGAToolbox, rtracklayer, scanMiR, scanMiRApp, scmeth, scruff, segmentSeq, SeqArray, seqCAT, seqsetvis, sevenC, SGSeq, ShortRead, signeR, SigsPack, SingleMoleculeFootprinting, sitadela, SNPhood, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.GRCh38, soGGi, SomaticSignatures, SparseSignatures, spatzie, spiky, SplicingGraphs, SPLINTER, srnadiff, STAN, strandCheckR, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, TAPseq, TarSeqQC, TCGAutils, TCGAWorkflow, TFBSTools, TitanCNA, TnT, trackViewer, transcriptR, tRNAscanImport, TSRchitect, TVTB, tximeta, Ularcirc, UMI4Cats, VanillaICE, VariantFiltering, VariantTools, VaSP, VplotR, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, YAPSA
Suggests Me	AnnotationForge, AnnotationHub, BindingSiteFinder, BiocOncoTK, chromswitch, ExperimentHubData, megadepth, methrix, parglms, plotgardener, QDNAseq, scTreeViz, splatter, systemPipeR, TFutils
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	GenomeInfoDb_1.30.1.tar.gz
Windows Binary	GenomeInfoDb_1.30.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	GenomeInfoDb_1.30.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomeInfoDb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomeInfoDb
Bioc Package Browser	https://code.bioconductor.org/browse/GenomeInfoDb/
Package Short Url	https://bioconductor.org/packages/GenomeInfoDb/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive