To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("AnnotationDbi")

In most cases, you don't need to download the package archive at all.

AnnotationDbi

   

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see AnnotationDbi.

Annotation Database Interface

Bioconductor version: 2.8

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: Biocore Team c/o BioC user list <bioconductor at stat.math.ethz.ch>

Citation (from within R, enter citation("AnnotationDbi")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("AnnotationDbi")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("AnnotationDbi")

 

PDF AnnotationDbi.pdf
PDF makeProbePackage.pdf
PDF NewSchema.pdf
PDF SQLForge.pdf
PDF   Reference Manual

Details

biocViews Annotation, Infrastructure, Software
Version 1.14.1
In Bioconductor since BioC 2.1 (R-2.6) (8.5 years)
License Artistic-2.0
Depends R (>= 2.7.0), methods, utils, Biobase(>= 1.17.0)
Imports methods, utils, Biobase, DBI, RSQLite
LinkingTo
Suggests DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, human.db0, hgu95av2cdf, affy, KEGG.db, XML
SystemRequirements
Enhances
URL
Depends On Me a4Base, a4Preproc, adme16cod.db, ag.db, agprobe, annotate, 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, chimp.db0, ChromHeatMap, citrusprobe, cottonprobe, DO.db, drosgenome1.db, drosgenome1probe, drosophila2.db, drosophila2probe, ecoli2.db, ecoli2probe, ecoliasv2probe, ecoliK12.db0, ecoliprobe, ecoliSakai.db0, eisa, 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, gene2pathway, GGdata, GGHumanMethCancerPanelv1.db, GO.db, 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, 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, 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, HuExExonProbesetLocation, HuExExonProbesetLocationHg18, HuExExonProbesetLocationHg19, hugene10stprobeset.db, hugene10sttranscriptcluster.db, hugene10stv1probe, hugene11stprobeset.db, hugene11sttranscriptcluster.db, human.db0, HuO22.db, hwgcod.db, illuminaHumanDASLBeadID.db, IlluminaHumanMethylation27k.db, IlluminaHumanMethylation450k.db, illuminaHumanv1.db, illuminaHumanv1BeadID.db, illuminaHumanv2.db, illuminaHumanv2BeadID.db, illuminaHumanv3.db, illuminaHumanv3BeadID.db, illuminaHumanv4.db, illuminaHumanv4BeadID.db, illuminaHumanWGDASLv3.db, illuminaHumanWGDASLv4.db, illuminaMousev1.db, illuminaMousev1BeadID.db, illuminaMousev1p1.db, illuminaMousev1p1BeadID.db, illuminaMousev2.db, illuminaMousev2BeadID.db, illuminaRatv1.db, illuminaRatv1BeadID.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, 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, MoExExonProbesetLocation, mogene10stprobeset.db, mogene10sttranscriptcluster.db, mogene10stv1probe, mogene11stprobeset.db, mogene11sttranscriptcluster.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, mwgcod.db, Norway981.db, nugohs1a520180.db, nugohs1a520180probe, nugomm1a520177.db, nugomm1a520177probe, oneChannelGUI, ontoTools, 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.Xl.eg.db, paeg1aprobe, PAnnBuilder, PartheenMetaData.db, pathRender, pedbarrayv10.db, pedbarrayv9.db, PFAM.db, PGSEA, pig.db0, plasmodiumanophelesprobe, POCRCannotation.db, poplarprobe, porcine.db, porcineprobe, r10kcod.db, rae230a.db, rae230aprobe, rae230b.db, rae230bprobe, RaExExonProbesetLocation, ragene10stprobeset.db, ragene10sttranscriptcluster.db, ragene10stv1probe, ragene11stprobeset.db, ragene11sttranscriptcluster.db, rat.db0, rat2302.db, rat2302probe, rattoxfxprobe, 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, saureusprobe, 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, annaffy, annotate, anopheles.db0, arabidopsis.db0, ath1121501.db, attract, BioNet, bovine.db, bovine.db0, canine.db, canine.db0, canine2.db, Category, celegans.db, cheung2010, chicken.db, chicken.db0, chimp.db0, ChromHeatMap, clusterProfiler, CoCiteStats, DO.db, domainsignatures, drosgenome1.db, drosophila2.db, ecoli2.db, ecoliK12.db0, ecoliSakai.db0, ExpressionView, fly.db0, gahgu133a.db, gahgu133b.db, gahgu133plus2.db, gahgu95av2.db, gahgu95b.db, gahgu95c.db, gahgu95d.db, gahgu95e.db, genefilter, geneplotter, GGBase, GGHumanMethCancerPanelv1.db, GGtools, GlobalAncova, globaltest, GO.db, GOSemSim, goseq, GOstats, GSEABase, h10kcod.db, h20kcod.db, hcg110.db, hgfocus.db, hgu133a.db, hgu133a2.db, hgu133b.db, hgu133plus2.db, hgu219.db, hgu95a.db, hgu95av2.db, hgu95b.db, hgu95c.db, hgu95d.db, hgu95e.db, hguatlas13k.db, hgubeta7.db, hguDKFZ31.db, hgug4100a.db, hgug4101a.db, hgug4110b.db, hgug4111a.db, hgug4112a.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, hs25kresogen.db, Hs6UG171.db, HsAgilentDesign026652.db, hthgu133a.db, hthgu133b.db, HTSanalyzeR, hu35ksuba.db, hu35ksubb.db, hu35ksubc.db, hu35ksubd.db, hu6800.db, hugene10stprobeset.db, hugene10sttranscriptcluster.db, hugene11stprobeset.db, hugene11sttranscriptcluster.db, human.db0, HuO22.db, hwgcod.db, illuminaHumanDASLBeadID.db, IlluminaHumanMethylation27k.db, IlluminaHumanMethylation450k.db, illuminaHumanv1.db, illuminaHumanv1BeadID.db, illuminaHumanv2.db, illuminaHumanv2BeadID.db, illuminaHumanv3.db, illuminaHumanv3BeadID.db, illuminaHumanv4.db, illuminaHumanv4BeadID.db, illuminaHumanWGDASLv3.db, illuminaHumanWGDASLv4.db, illuminaMousev1.db, illuminaMousev1BeadID.db, illuminaMousev1p1.db, illuminaMousev1p1BeadID.db, illuminaMousev2.db, illuminaMousev2BeadID.db, illuminaRatv1.db, illuminaRatv1BeadID.db, indac.db, JazaeriMetaData.db, KEGG.db, keggorthology, LAPOINTE.db, lumi, lumiHumanAll.db, lumiHumanIDMapping, lumiMouseAll.db, lumiMouseIDMapping, lumiRatAll.db, lumiRatIDMapping, m10kcod.db, m20kcod.db, malaria.db0, methylumi, mgu74a.db, mgu74av2.db, mgu74b.db, mgu74bv2.db, mgu74c.db, mgu74cv2.db, mguatlas5k.db, mgug4104a.db, mgug4120a.db, mgug4121a.db, mgug4122a.db, mi16cod.db, mirbase.db, mm24kresogen.db, MmAgilentDesign026655.db, moe430a.db, moe430b.db, mogene10stprobeset.db, mogene10sttranscriptcluster.db, mogene11stprobeset.db, mogene11sttranscriptcluster.db, mouse.db0, mouse4302.db, mouse430a2.db, mpedbarray.db, mu11ksuba.db, mu11ksubb.db, Mu15v1.db, mu19ksuba.db, mu19ksubb.db, mu19ksubc.db, Mu22v3.db, mwgcod.db, Norway981.db, nugohs1a520180.db, nugomm1a520177.db, 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.Xl.eg.db, PAnnBuilder, PartheenMetaData.db, PatientGeneSets, PCpheno, pedbarrayv10.db, pedbarrayv9.db, PFAM.db, phenoTest, pig.db0, POCRCannotation.db, porcine.db, qpgraph, r10kcod.db, rae230a.db, rae230b.db, ragene10stprobeset.db, ragene10sttranscriptcluster.db, ragene11stprobeset.db, ragene11sttranscriptcluster.db, rat.db0, rat2302.db, reactome.db, rgu34a.db, rgu34b.db, rgu34c.db, rguatlas4k.db, rgug4105a.db, rgug4130a.db, rgug4131a.db, rhesus.db0, ri16cod.db, RmiR.Hs.miRNA, RmiR.hsa, RnAgilentDesign028282.db, rnu34.db, Roberts2005Annotation.db, rtu34.db, rwgcod.db, safe, ScISI, SHDZ.db, SLGI, targetscan.Hs.eg.db, targetscan.Mm.eg.db, tigre, topGO, u133x3p.db, worm.db0, xenopus.db0, xlaevis.db, yeast.db0, yeast2.db, ygs98.db, zebrafish.db, zebrafish.db0
Suggests Me BiocCaseStudies, ExpressionView, GeneAnswers, GeneRegionScan, sigPathway
Build Report  

Package Archives

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

Package Source AnnotationDbi_1.14.1.tar.gz
Windows Binary AnnotationDbi_1.14.1.zip
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/AnnotationDbi/tree/release-2.8
Package Short Url http://bioconductor.org/packages/AnnotationDbi/
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