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>

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