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>

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: How to use the ".db" annotation packages
PDF R Script Creating an annotation package with a new database schema
PDF R Script Creating probe packages
PDF R Script SQLForge: An easy way to create a new annotation package with a standard database schema.
PDF   Reference Manual

Details

biocViews Annotation, Infrastructure
Depends R (>= 2.7.0), methods, utils, Biobase(>= 1.17.0)
Imports methods, utils, Biobase, DBI, RSQLite
Suggests DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, human.db0, hgu95av2cdf, affy, KEGG.db, XML
System Requirements
License Artistic-2.0
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
Version 1.14.1
Since Bioconductor 2.1 (R-2.6)

Package Downloads

Package Source AnnotationDbi_1.14.1.tar.gz
Windows Binary AnnotationDbi_1.14.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary AnnotationDbi_1.14.1.tgz
Package Downloads Report Download Stats

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