GenomeInfoDb

DOI: 10.18129/B9.bioc.GenomeInfoDb    

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

Bioconductor version: Release (3.15)

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, Martin Morgan, Marc Carlson, H. Pagès

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version 1.32.4
In Bioconductor since BioC 2.14 (R-3.1) (8.5 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
LinkingTo
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
SystemRequirements
Enhances
URL https://bioconductor.org/packages/GenomeInfoDb
BugReports https://github.com/Bioconductor/GenomeInfoDb/issues
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, UCSCRepeatMasker, VariantAnnotation, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me AllelicImbalance, alpine, amplican, AneuFinder, AnnotationHubData, annotatr, ASpediaFI, ATACseqQC, atena, BaalChIP, ballgown, bambu, BasicSTARRseq, BioPlex, 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, comapr, compEpiTools, consensusSeekeR, conumee, CopyNumberPlots, CopywriteR, crisprBowtie, crisprBwa, CRISPRseek, CrispRVariants, csaw, customProDB, DAMEfinder, dasper, decompTumor2Sig, DeepBlueR, derfinder, derfinderPlot, DEScan2, DEWSeq, diffHic, diffloop, diffUTR, DMRcate, DMRScan, dmrseq, DominoEffect, easyRNASeq, ELMER, enhancerHomologSearch, enrichTF, ensembldb, ensemblVEP, epialleleR, epigenomix, epigraHMM, EpiTxDb, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomeCopy, exomePeak2, extraChIPs, FindIT2, fitCons.UCSC.hg19, FLAMES, FRASER, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, GenoGAM, genomation, genomeIntervals, GenomicDistributions, GenomicDistributionsData, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicScores, GenomicState, genotypeeval, GenVisR, ggbio, gmoviz, GOTHiC, GRaNIE, 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, MafH5.gnomAD.v3.1.2.GRCh38, maser, metagene, metagene2, metaseqR2, metavizr, MethCP, methimpute, methInheritSim, methylKit, methylPipe, MethylSeqData, methylSig, methylumi, minfi, MinimumDistance, MMAPPR2, monaLisa, mosaics, Motif2Site, motifbreakR, motifmatchr, MouseFM, msgbsR, multicrispr, multiHiCcompare, MungeSumstats, musicatk, MutationalPatterns, myvariant, NADfinder, nearBynding, netDx, normr, nucleR, nullranges, NxtIRFcore, ODER, OGRE, 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, rfPred, RiboCrypt, RiboProfiling, riboSeqR, ribosomeProfilingQC, RJMCMCNucleosomes, RLSeq, rnaEditr, RNAmodR, roar, RTCGAToolbox, rtracklayer, scanMiR, scanMiRApp, scDblFinder, scmeth, scruff, segmentSeq, SeqArray, seqCAT, seqsetvis, sesame, sesameData, 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, SNPlocs.Hsapiens.dbSNP155.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, epimutacions, ExperimentHubData, fishpond, megadepth, methrix, parglms, plotgardener, QDNAseq, scTreeViz, splatter, systemPipeR, TFutils, xcoredata
Links To Me
Build Report  

Package Archives

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

Source Package GenomeInfoDb_1.32.4.tar.gz
Windows Binary GenomeInfoDb_1.32.4.zip (64-bit only)
macOS Binary (x86_64) GenomeInfoDb_1.32.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomeInfoDb
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomeInfoDb
Package Short Url https://bioconductor.org/packages/GenomeInfoDb/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: