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GenomeInfoDb

This is the development version of GenomeInfoDb; for the stable release version, see GenomeInfoDb.

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


Bioconductor version: Development (3.19)

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, enter citation("GenomeInfoDb")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version 1.39.13
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, UCSC.utils, GenomeInfoDbData
System Requirements
URL https://bioconductor.org/packages/GenomeInfoDb
Bug Reports https://github.com/Bioconductor/GenomeInfoDb/issues
See More
Suggests R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, 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 Me Biostrings, BRGenomics, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenomeForge, bumphunter, ChIPComp, CODEX, CSAR, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, IdeoViz, Rsamtools, SCOPE, txdbmaker, UCSCRepeatMasker, VariantAnnotation
Imports Me alabaster.ranges, AllelicImbalance, amplican, AneuFinder, AnnotationHubData, annotatr, ATACseqQC, ATACseqTFEA, atena, BaalChIP, ballgown, bambu, BasicSTARRseq, BindingSiteFinder, BioPlex, biovizBase, biscuiteer, BiSeq, bnbc, branchpointer, breakpointR, bsseq, BUSpaRse, CAGEfightR, cageminer, CAGEr, cardelino, casper, cBioPortalData, CexoR, cfdnakit, cfDNAPro, 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, crisprBowtie, crisprBwa, crisprDesign, CRISPRseek, crisprShiny, CrispRVariants, crisprViz, csaw, customProDB, DAMEfinder, decompTumor2Sig, DegCre, demuxSNP, derfinder, derfinderPlot, DEScan2, DEWSeq, diffHic, diffUTR, DMRcate, DMRScan, dmrseq, DominoEffect, easylift, easyRNASeq, ELMER, enhancerHomologSearch, enrichTF, ensembldb, ensemblVEP, epialleleR, EpiCompare, epigenomix, epigraHMM, EpiMix, epimutacions, EpiTxDb, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomePeak2, extraChIPs, factR, FindIT2, fitCons.UCSC.hg19, FLAMES, FRASER, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, gDNAx, geneAttribution, genomation, GenomAutomorphism, genomeIntervals, GenomicDistributions, GenomicDistributionsData, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicPlot, GenomicScores, GenomicState, GenVisR, ggbio, gmoviz, GOTHiC, GRaNIE, grasp2db, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCBricks, HiCDCPlus, HiCDOC, HiCExperiment, HiContacts, HiTC, HTSeqGenie, idr2d, IMAS, InPAS, INSPEcT, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, katdetectr, 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.v3.1.2.GRCh38, MafH5.gnomAD.v4.0.GRCh38, mariner, maser, metagene, metagene2, metaseqR2, methimpute, methInheritSim, methodical, methylKit, methylPipe, MethylSeqData, methylSig, methylumi, minfi, MinimumDistance, MMAPPR2, mobileRNA, monaLisa, mosaics, Motif2Site, motifbreakR, motifmatchr, motifTestR, MouseFM, msgbsR, multicrispr, multiHiCcompare, MungeSumstats, musicatk, MutationalPatterns, myvariant, NADfinder, nearBynding, netDx, NoRCE, normr, nucleR, nullranges, OGRE, OMICsPCA, ORFik, Organism.dplyr, panelcn.mops, periodicDNA, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, pipeFrame, plotgardener, plyinteractions, plyranges, podkat, pram, prebs, proActiv, profileplyr, ProteoDisco, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, raer, RaggedExperiment, RareVariantVis, RCAS, rCGH, RcisTarget, recount, recoup, regioneR, regionReport, REMP, Repitools, RESOLVE, rfPred, RgnTX, rGREAT, RiboCrypt, RiboProfiling, riboSeqR, ribosomeProfilingQC, RJMCMCNucleosomes, RLSeq, rnaEditr, RNAmodR, roar, RTCGAToolbox, rtracklayer, scanMiR, scanMiRApp, scDblFinder, scmeth, scRNAseqApp, scruff, segmentSeq, seqArchRplus, SeqArray, seqCAT, seqsetvis, sesame, sesameData, sevenC, SGSeq, ShortRead, signeR, SigsPack, SingleMoleculeFootprinting, sitadela, SNPhood, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, soGGi, SomaticSignatures, SOMNiBUS, SparseSignatures, spatzie, spiky, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, tadar, TAPseq, TCGAutils, TCGAWorkflow, TEKRABber, TENxIO, TFBSTools, tidyCoverage, TitanCNA, TnT, trackViewer, transcriptR, transmogR, tRNAscanImport, TVTB, tximeta, Ularcirc, UMI4Cats, VanillaICE, VariantFiltering, VariantTools, VaSP, VplotR, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, YAPSA
Suggests Me AlphaMissenseR, AnnotationForge, AnnotationHub, BiocOncoTK, BioMartGOGeneSets, DiffBind, ExperimentHubData, fishpond, ldblock, megadepth, methrix, parglms, QDNAseq, RAIDS, regioneReloaded, scTreeViz, seqpac, splatter, systemPipeR, TFutils, UCSC.utils, xcoredata
Links To Me
Build Report Build Report

Package Archives

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

Source Package GenomeInfoDb_1.39.13.tar.gz
Windows Binary GenomeInfoDb_1.39.13.zip (64-bit only)
macOS Binary (x86_64) GenomeInfoDb_1.39.13.tgz
macOS Binary (arm64) GenomeInfoDb_1.39.13.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