GenomeInfoDb

DOI: 10.18129/B9.bioc.GenomeInfoDb  

This package is for version 3.17 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

Bioconductor version: 3.17

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 "4.3") 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
HTML R Script Submitting your organism to GenomeInfoDb
PDF   Reference Manual
Text   NEWS
Video   Simple tasks genomeInfoDb

Details

biocViews Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version 1.36.4
In Bioconductor since BioC 2.14 (R-3.1) (9.5 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, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenomeForge, bumphunter, ChIPComp, CODEX, CSAR, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, IdeoViz, Rsamtools, SCOPE, UCSCRepeatMasker, VariantAnnotation
Imports Me alabaster.ranges, AllelicImbalance, alpine, amplican, AneuFinder, AnnotationHubData, annotatr, ASpediaFI, ATACseqQC, ATACseqTFEA, atena, BaalChIP, ballgown, bambu, BasicSTARRseq, BindingSiteFinder, BioPlex, biovizBase, biscuiteer, BiSeq, bnbc, branchpointer, breakpointR, BSgenome, bsseq, BUSpaRse, CAGEfightR, cageminer, CAGEr, cardelino, casper, cBioPortalData, CexoR, 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, CopywriteR, crisprBowtie, crisprBwa, crisprDesign, CRISPRseek, CrispRVariants, crisprViz, csaw, customProDB, DAMEfinder, dasper, decompTumor2Sig, DeepBlueR, derfinder, derfinderPlot, DEScan2, DEWSeq, diffHic, diffUTR, DMRcate, DMRScan, dmrseq, DominoEffect, easyRNASeq, ELMER, enhancerHomologSearch, enrichTF, ensembldb, ensemblVEP, epialleleR, EpiCompare, epigenomix, epigraHMM, EpiMix, epimutacions, EpiTxDb, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomeCopy, exomePeak2, extraChIPs, factR, FindIT2, fitCons.UCSC.hg19, FLAMES, FRASER, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, genomation, GenomAutomorphism, genomeIntervals, GenomicDistributions, GenomicDistributionsData, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicScores, GenomicState, genotypeeval, 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.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, mariner, 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, NoRCE, 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, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, 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, SparseSignatures, spatzie, spiky, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, STAN, strandCheckR, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, TAPseq, TarSeqQC, TCGAutils, TCGAWorkflow, TENxIO, TFBSTools, TitanCNA, TnT, trackViewer, transcriptR, tRNAscanImport, TVTB, tximeta, Ularcirc, UMI4Cats, VanillaICE, VariantFiltering, VariantTools, VaSP, VplotR, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, YAPSA
Suggests Me AnnotationForge, AnnotationHub, BiocOncoTK, BioMartGOGeneSets, chromswitch, DiffBind, ExperimentHubData, fishpond, ldblock, megadepth, methrix, parglms, plotgardener, QDNAseq, regioneReloaded, scTreeViz, seqpac, 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_1.36.4.tar.gz
Windows Binary GenomeInfoDb_1.36.4.zip
macOS Binary (x86_64) GenomeInfoDb_1.36.4.tgz
macOS Binary (arm64) GenomeInfoDb_1.36.4.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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