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>

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