GenomeInfoDb

This package is for version 3.9 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: 3.9

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 "3.6") 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 1.20.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License Artistic-2.0
Depends R (>= 3.1), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12)
Imports stats, stats4, utils, RCurl, GenomeInfoDbData
System Requirements
URL
See More
Suggests GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr
Linking To
Enhances
Depends On Me BSgenome, bumphunter, ChIPComp, CODEX, CSAR, eQTL, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, htSeqTools, IdeoViz, methyAnalysis, MTseeker, Rsamtools, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, VariantAnnotation, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me AllelicImbalance, alpine, amplican, AneuFinder, AnnotationHubData, annotatr, ATACseqQC, BaalChIP, ballgown, BasicSTARRseq, biovizBase, BiSeq, bnbc, branchpointer, breakpointR, BSgenome, bsseq, CAGEfightR, CAGEr, casper, CexoR, chimeraviz, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPpeakAnno, ChIPseeker, chromstaR, chromVAR, CINdex, cleanUpdTSeq, cn.mops, CNEr, CNPBayes, CNVPanelizer, CNVRanger, compEpiTools, consensusSeekeR, conumee, CopyNumberPlots, CopywriteR, CrispRVariants, csaw, customProDB, DeepBlueR, derfinder, derfinderPlot, DEScan2, diffHic, diffloop, DMRScan, dmrseq, DominoEffect, easyRNASeq, ELMER, enrichTF, ensembldb, ensemblVEP, epigenomix, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomeCopy, fitCons.UCSC.hg19, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, GenoGAM, genomation, genomeIntervals, GenomicFiles, GenomicInteractions, GenomicScores, genoset, genotypeeval, GenVisR, ggbio, GGtools, gQTLstats, grasp2db, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCBricks, HiTC, HTSeqGenie, IMAS, InPAS, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, ldblock, MACPET, MADSEQ, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.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.r2.0.1.GRCh38, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.0.1.GRCh38, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, maser, metagene, metagene2, metavizr, methimpute, methInheritSim, methylKit, methylPipe, methylumi, methyvim, minfi, MinimumDistance, mosaics, motifbreakR, motifmatchr, msgbsR, MTseekerData, multiHiCcompare, MutationalPatterns, myvariant, NADfinder, NarrowPeaks, normr, nucleR, OMICsPCA, ORFik, Organism.dplyr, panelcn.mops, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, pipeFrame, plyranges, podkat, pram, prebs, profileplyr, ProteomicsAnnotationHubData, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, RaggedExperiment, RareVariantVis, Rariant, Rcade, RCAS, rCGH, recount, regioneR, regionReport, REMP, Repitools, RiboProfiling, riboSeqR, RJMCMCNucleosomes, roar, RTCGAToolbox, rtracklayer, scmeth, scruff, segmentSeq, SeqArray, seqCAT, seqplots, seqsetvis, sevenC, SGSeq, ShortRead, SNPchip, 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, SplicingGraphs, SPLINTER, srnadiff, STAN, strandCheckR, SummarizedExperiment, TarSeqQC, TCGAbiolinks, TCGAutils, TCGAWorkflow, TFBSTools, TitanCNA, TnT, trackViewer, transcriptR, tRNAscanImport, TSRchitect, TVTB, tximeta, TxRegInfra, Ularcirc, VanillaICE, VariantFiltering, VariantTools, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, YAPSA, yriMulti
Suggests Me AnnotationForge, AnnotationHub, BiocOncoTK, chromswitch, ExperimentHubData, gQTLBase, parglms, QDNAseq, recoup, StructuralVariantAnnotation, TFutils
Links To Me
Build Report Build Report

Package Archives

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

Source Package GenomeInfoDb_1.20.0.tar.gz
Windows Binary GenomeInfoDb_1.20.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) GenomeInfoDb_1.20.0.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 3.9 Source Archive