AnnotationDbi

Annotation Database Interface

Bioconductor version: Development (3.0)

Provides user interface and database connection code for annotation data packages using SQLite data storage.

Author: Herve Pages, Marc Carlson, Seth Falcon, Nianhua Li

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("AnnotationDbi")

To cite this package in a publication, start R and enter:

    citation("AnnotationDbi")

Documentation

PDF R Script AnnotationDbi: Introduction To Bioconductor Annotation Packages
PDF R Script How to use bimaps from the ".db" annotation packages
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Infrastructure, Software
Version 1.27.1
In Bioconductor since BioC 2.1 (R-2.6)
License Artistic-2.0
Depends R (>= 2.7.0), methods, utils, BiocGenerics(>= 0.5.4), Biobase(>= 1.17.0), GenomeInfoDb(>= 0.99.17)
Imports methods, utils, DBI, RSQLite, BiocGenerics, Biobase, S4Vectors, IRanges
Suggests DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, seqnames.db, reactome.db, AnnotationForge, graph, org.TguttataTestingSubset.eg.db, BiocStyle, knitr
System Requirements
URL
Depends On Me a4Base, a4Preproc, adme16cod.db, affylmGUI, ag.db, agprobe, annotate, AnnotationForge, AnnotationFuncs, anopheles.db0, arabidopsis.db0, ath1121501.db, ath1121501probe, attract, barley1probe, bovine.db, bovine.db0, bovineprobe, bsubtilisprobe, canine.db, canine.db0, canine2.db, canine2probe, canineprobe, Category, celegans.db, celegansprobe, chicken.db, chicken.db0, chickenprobe, chimera, chimp.db0, ChromHeatMap, citrusprobe, cottonprobe, customProDB, DO.db, drosgenome1.db, drosgenome1probe, drosophila2.db, drosophila2probe, ecoli2.db, ecoli2probe, ecoliasv2probe, ecoliK12.db0, ecoliprobe, ecoliSakai.db0, eisa, ExpressionView, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, fly.db0, gahgu133a.db, gahgu133aprobe, gahgu133b.db, gahgu133bprobe, gahgu133plus2.db, gahgu133plus2probe, gahgu95av2.db, gahgu95av2probe, gahgu95b.db, gahgu95bprobe, gahgu95c.db, gahgu95cprobe, gahgu95d.db, gahgu95dprobe, gahgu95e.db, gahgu95eprobe, GenomicFeatures, GGdata, GGHumanMethCancerPanelv1.db, GO.db, GOFunction, goProfiles, h10kcod.db, h20kcod.db, hcg110.db, hcg110probe, hgfocus.db, hgfocusprobe, hgu133a.db, hgu133a2.db, hgu133a2probe, hgu133aprobe, hgu133atagprobe, hgu133b.db, hgu133bprobe, hgu133plus2.db, hgu133plus2probe, hgu219.db, hgu219probe, hgu95a.db, hgu95aprobe, hgu95av2.db, hgu95av2probe, hgu95b.db, hgu95bprobe, hgu95c.db, hgu95cprobe, hgu95d.db, hgu95dprobe, hgu95e.db, hgu95eprobe, hguatlas13k.db, hgubeta7.db, hguDKFZ31.db, hgug4100a.db, hgug4101a.db, hgug4110b.db, hgug4111a.db, hgug4112a.db, hgug4845a.db, hguqiagenv3.db, hi16cod.db, hom.At.inp.db, hom.Ce.inp.db, hom.Dm.inp.db, hom.Dr.inp.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, Homo.sapiens, hs25kresogen.db, Hs6UG171.db, HsAgilentDesign026652.db, hthgu133a.db, hthgu133aprobe, hthgu133b.db, hthgu133bprobe, hthgu133pluspmprobe, htmg430aprobe, htmg430bprobe, htmg430pmprobe, htrat230pmprobe, htratfocusprobe, hu35ksuba.db, hu35ksubaprobe, hu35ksubb.db, hu35ksubbprobe, hu35ksubc.db, hu35ksubcprobe, hu35ksubd.db, hu35ksubdprobe, hu6800.db, hu6800probe, huex10stprobeset.db, huex10sttranscriptcluster.db, HuExExonProbesetLocation, HuExExonProbesetLocationHg18, HuExExonProbesetLocationHg19, hugene10stprobeset.db, hugene10sttranscriptcluster.db, hugene10stv1probe, hugene11stprobeset.db, hugene11sttranscriptcluster.db, hugene20stprobeset.db, hugene20sttranscriptcluster.db, hugene21stprobeset.db, hugene21sttranscriptcluster.db, human.db0, HuO22.db, hwgcod.db, IlluminaHumanMethylation27k.db, IlluminaHumanMethylation450k.db, IlluminaHumanMethylation450kprobe, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv2BeadID.db, illuminaHumanv3.db, illuminaHumanv4.db, illuminaHumanWGDASLv3.db, illuminaHumanWGDASLv4.db, illuminaMousev1.db, illuminaMousev1p1.db, illuminaMousev2.db, illuminaRatv1.db, indac.db, JazaeriMetaData.db, KEGG.db, LAPOINTE.db, lumiHumanAll.db, lumiHumanIDMapping, lumiMouseAll.db, lumiMouseIDMapping, lumiRatAll.db, lumiRatIDMapping, m10kcod.db, m20kcod.db, maizeprobe, malaria.db0, maPredictDSC, medicagoprobe, mgu74a.db, mgu74aprobe, mgu74av2.db, mgu74av2probe, mgu74b.db, mgu74bprobe, mgu74bv2.db, mgu74bv2probe, mgu74c.db, mgu74cprobe, mgu74cv2.db, mgu74cv2probe, mguatlas5k.db, mgug4104a.db, mgug4120a.db, mgug4121a.db, mgug4122a.db, mi16cod.db, mirbase.db, mirna10probe, MLP, mm24kresogen.db, MmAgilentDesign026655.db, moe430a.db, moe430aprobe, moe430b.db, moe430bprobe, moex10stprobeset.db, moex10sttranscriptcluster.db, MoExExonProbesetLocation, mogene10stprobeset.db, mogene10sttranscriptcluster.db, mogene10stv1probe, mogene11stprobeset.db, mogene11sttranscriptcluster.db, mogene20stprobeset.db, mogene20sttranscriptcluster.db, mogene21stprobeset.db, mogene21sttranscriptcluster.db, mouse.db0, mouse4302.db, mouse4302probe, mouse430a2.db, mouse430a2probe, mpedbarray.db, mu11ksuba.db, mu11ksubaprobe, mu11ksubb.db, mu11ksubbprobe, Mu15v1.db, mu19ksuba.db, mu19ksubb.db, mu19ksubc.db, Mu22v3.db, Mus.musculus, mwgcod.db, Norway981.db, nugohs1a520180.db, nugohs1a520180probe, nugomm1a520177.db, nugomm1a520177probe, OperonHumanV3.db, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Hs.ipi.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Sco.eg.db, org.Ss.eg.db, org.Tgondii.eg.db, org.Xl.eg.db, OrganismDbi, PADOG, paeg1aprobe, PAnnBuilder, PANTHER.db, PartheenMetaData.db, pathRender, pedbarrayv10.db, pedbarrayv9.db, PFAM.db, PGSEA, pig.db0, plasmodiumanophelesprobe, POCRCannotation.db, poplarprobe, porcine.db, porcineprobe, primeviewprobe, r10kcod.db, rae230a.db, rae230aprobe, rae230b.db, rae230bprobe, raex10stprobeset.db, raex10sttranscriptcluster.db, RaExExonProbesetLocation, ragene10stprobeset.db, ragene10sttranscriptcluster.db, ragene10stv1probe, ragene11stprobeset.db, ragene11sttranscriptcluster.db, ragene20stprobeset.db, ragene20sttranscriptcluster.db, ragene21stprobeset.db, ragene21sttranscriptcluster.db, rat.db0, rat2302.db, rat2302probe, rattoxfxprobe, Rattus.norvegicus, reactome.db, Resourcerer, rgu34a.db, rgu34aprobe, rgu34b.db, rgu34bprobe, rgu34c.db, rgu34cprobe, rguatlas4k.db, rgug4105a.db, rgug4130a.db, rgug4131a.db, rhesus.db0, rhesusprobe, ri16cod.db, riceprobe, RnAgilentDesign028282.db, rnu34.db, rnu34probe, Roberts2005Annotation.db, RpsiXML, rtu34.db, rtu34probe, rwgcod.db, safe, saureusprobe, seqnames.db, SHDZ.db, soybeanprobe, sugarcaneprobe, targetscan.Hs.eg.db, targetscan.Mm.eg.db, test3probe, tinesath1probe, tomatoprobe, topGO, u133x3p.db, u133x3pprobe, vitisviniferaprobe, wheatprobe, worm.db0, xenopus.db0, xenopuslaevisprobe, xlaevis.db, xlaevis2probe, xtropicalisprobe, yeast.db0, yeast2.db, yeast2probe, ygs98.db, ygs98probe, zebrafish.db, zebrafish.db0, zebrafishprobe
Imports Me adme16cod.db, adSplit, affycoretools, ag.db, agcdf, AllelicImbalance, annaffy, AnnotationHub, anopheles.db0, arabidopsis.db0, ath1121501.db, ath1121501cdf, attract, barley1cdf, beadarray, biomaRt, BioNet, biovizBase, bovine.db, bovine.db0, bovinecdf, bsubtiliscdf, CancerMutationAnalysis, canine.db, canine.db0, canine2.db, canine2cdf, caninecdf, Category, categoryCompare, celegans.db, celeganscdf, cheung2010, chicken.db, chicken.db0, chickencdf, chimp.db0, ChIPpeakAnno, ChIPseeker, citruscdf, clusterProfiler, CoCiteStats, cottoncdf, customProDB, cyp450cdf, DeSousa2013, DO.db, domainsignatures, DOSE, drosgenome1.db, drosgenome1cdf, drosophila2.db, drosophila2cdf, ecoli2.db, ecoli2cdf, ecoliasv2cdf, ecolicdf, ecoliK12.db0, ecoliSakai.db0, ExpressionView, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, fly.db0, FunciSNP, gage, gahgu133a.db, gahgu133b.db, gahgu133plus2.db, gahgu95av2.db, gahgu95b.db, gahgu95c.db, gahgu95d.db, gahgu95e.db, gCMAP, gCMAPWeb, genefilter, geneplotter, GGBase, GGHumanMethCancerPanelv1.db, GGtools, GlobalAncova, globaltest, GO.db, GOFunction, GOSemSim, goseq, GOSim, GOstats, goTools, gp53cdf, graphite, GSEABase, Gviz, h10kcod.db, h20kcod.db, hcg110.db, hcg110cdf, hgfocus.db, hgfocuscdf, hgu133a.db, hgu133a2.db, hgu133a2cdf, hgu133acdf, hgu133atagcdf, hgu133b.db, hgu133bcdf, hgu133plus2.db, hgu133plus2cdf, hgu219.db, hgu219cdf, hgu95a.db, hgu95acdf, hgu95av2.db, hgu95av2cdf, hgu95b.db, hgu95bcdf, hgu95c.db, hgu95ccdf, hgu95d.db, hgu95dcdf, hgu95e.db, hgu95ecdf, hguatlas13k.db, hgubeta7.db, hguDKFZ31.db, hgug4100a.db, hgug4101a.db, hgug4110b.db, hgug4111a.db, hgug4112a.db, hgug4845a.db, hguqiagenv3.db, hi16cod.db, hivprtplus2cdf, hom.At.inp.db, hom.Ce.inp.db, hom.Dm.inp.db, hom.Dr.inp.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, Homo.sapiens, hs25kresogen.db, Hs6UG171.db, HsAgilentDesign026652.db, hthgu133a.db, hthgu133acdf, hthgu133b.db, hthgu133bcdf, hthgu133pluspmcdf, htmg430acdf, htmg430bcdf, htmg430pmcdf, htrat230pmcdf, htratfocuscdf, HTSanalyzeR, hu35ksuba.db, hu35ksubacdf, hu35ksubb.db, hu35ksubbcdf, hu35ksubc.db, hu35ksubccdf, hu35ksubd.db, hu35ksubdcdf, hu6800.db, hu6800cdf, hu6800subacdf, hu6800subbcdf, hu6800subccdf, hu6800subdcdf, huex10stprobeset.db, huex10sttranscriptcluster.db, hugene10stprobeset.db, hugene10sttranscriptcluster.db, hugene10stv1cdf, hugene11stprobeset.db, hugene11sttranscriptcluster.db, hugene20stprobeset.db, hugene20sttranscriptcluster.db, hugene21stprobeset.db, hugene21sttranscriptcluster.db, human.db0, HuO22.db, hwgcod.db, IlluminaHumanMethylation27k.db, IlluminaHumanMethylation450k.db, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv2BeadID.db, illuminaHumanv3.db, illuminaHumanv4.db, illuminaHumanWGDASLv3.db, illuminaHumanWGDASLv4.db, illuminaMousev1.db, illuminaMousev1p1.db, illuminaMousev2.db, illuminaRatv1.db, indac.db, interactiveDisplay, JazaeriMetaData.db, KEGG.db, keggorthology, KEGGprofile, LAPOINTE.db, lumi, lumiHumanAll.db, lumiHumanIDMapping, lumiMouseAll.db, lumiMouseIDMapping, lumiRatAll.db, lumiRatIDMapping, m10kcod.db, m20kcod.db, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, maizecdf, malaria.db0, medicagocdf, MeSHDbi, methyAnalysis, methylumi, mgu74a.db, mgu74acdf, mgu74av2.db, mgu74av2cdf, mgu74b.db, mgu74bcdf, mgu74bv2.db, mgu74bv2cdf, mgu74c.db, mgu74ccdf, mgu74cv2.db, mgu74cv2cdf, mguatlas5k.db, mgug4104a.db, mgug4120a.db, mgug4121a.db, mgug4122a.db, mi16cod.db, MineICA, MiRaGE, mirbase.db, mirna102xgaincdf, mirna10cdf, mirna20cdf, mm24kresogen.db, MmAgilentDesign026655.db, moe430a.db, moe430acdf, moe430b.db, moe430bcdf, moex10stprobeset.db, moex10sttranscriptcluster.db, mogene10stprobeset.db, mogene10sttranscriptcluster.db, mogene10stv1cdf, mogene11stprobeset.db, mogene11sttranscriptcluster.db, mogene20stprobeset.db, mogene20sttranscriptcluster.db, mogene21stprobeset.db, mogene21sttranscriptcluster.db, mouse.db0, mouse4302.db, mouse4302cdf, mouse430a2.db, mouse430a2cdf, mpedbarray.db, mu11ksuba.db, mu11ksubacdf, mu11ksubb.db, mu11ksubbcdf, Mu15v1.db, mu19ksuba.db, mu19ksubacdf, mu19ksubb.db, mu19ksubbcdf, mu19ksubc.db, mu19ksubccdf, Mu22v3.db, mu6500subacdf, mu6500subbcdf, mu6500subccdf, mu6500subdcdf, Mus.musculus, mwgcod.db, Norway981.db, nugohs1a520180.db, nugohs1a520180cdf, nugomm1a520177.db, nugomm1a520177cdf, OperonHumanV3.db, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Hs.ipi.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Sco.eg.db, org.Ss.eg.db, org.Tgondii.eg.db, org.Xl.eg.db, OrganismDbi, PADOG, paeg1acdf, PAnnBuilder, PANTHER.db, PartheenMetaData.db, pathview, pcaGoPromoter, PCpheno, pedbarrayv10.db, pedbarrayv9.db, PFAM.db, phenoTest, pig.db0, plasmodiumanophelescdf, POCRCannotation.db, PolyPhen.Hsapiens.dbSNP131, poplarcdf, porcine.db, porcinecdf, ppiData, primeviewcdf, qpgraph, r10kcod.db, rae230a.db, rae230acdf, rae230b.db, rae230bcdf, raex10stprobeset.db, raex10sttranscriptcluster.db, ragene10stprobeset.db, ragene10sttranscriptcluster.db, ragene10stv1cdf, ragene11stprobeset.db, ragene11sttranscriptcluster.db, ragene20stprobeset.db, ragene20sttranscriptcluster.db, ragene21stprobeset.db, ragene21sttranscriptcluster.db, rat.db0, rat2302.db, rat2302cdf, rattoxfxcdf, Rattus.norvegicus, reactome.db, ReactomePA, REDseq, ReportingTools, rgu34a.db, rgu34acdf, rgu34b.db, rgu34bcdf, rgu34c.db, rgu34ccdf, rguatlas4k.db, rgug4105a.db, rgug4130a.db, rgug4131a.db, rhesus.db0, rhesuscdf, ri16cod.db, ricecdf, RmiR.Hs.miRNA, RmiR.hsa, RnAgilentDesign028282.db, rnu34.db, rnu34cdf, Roberts2005Annotation.db, rTRM, rtu34.db, rtu34cdf, rwgcod.db, saureuscdf, ScISI, seqnames.db, SHDZ.db, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, SLGI, soybeancdf, sugarcanecdf, targetscan.Hs.eg.db, targetscan.Mm.eg.db, test1cdf, test2cdf, test3cdf, tigre, tomatocdf, topGO, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Athaliana.BioMart.plantsmart14, TxDb.Athaliana.BioMart.plantsmart16, TxDb.Athaliana.BioMart.plantsmart19, TxDb.Athaliana.BioMart.plantsmart21, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, u133aaofav2cdf, u133x3p.db, u133x3pcdf, UniProt.ws, VariantAnnotation, VariantFiltering, virtualArray, vitisviniferacdf, wheatcdf, worm.db0, xenopus.db0, xenopuslaeviscdf, xlaevis.db, xlaevis2cdf, xtropicaliscdf, ye6100subacdf, ye6100subbcdf, ye6100subccdf, ye6100subdcdf, yeast.db0, yeast2.db, yeast2cdf, ygs98.db, ygs98cdf, zebrafish.db, zebrafish.db0, zebrafishcdf
Suggests Me BiocCaseStudies, BiocGenerics, GeneAnswers, GeneRegionScan, GenomicRanges, limma, MmPalateMiRNA, neaGUI, oneChannelGUI, qcmetrics, sigPathway

Package Downloads

Package Source AnnotationDbi_1.27.1.tar.gz
Windows Binary AnnotationDbi_1.27.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) AnnotationDbi_1.27.1.tgz
Mac OS X 10.9 (Mavericks)
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