AnnotationDbi
Annotation Database Interface
Bioconductor version: 2.7
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
SQLForge: An easy way to create a new annotation package with a standard database schema.
Details
Depends
R (>= 2.7.0), methods, utils,
Biobase(>= 1.17.0)
System Requirements
License
Artistic-2.0
Depends On Me
adme16cod.db,
ag.db,
agprobe,
annotate,
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,
GOSemSim,
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,
HuExExonProbesetLocationHg18,
HuExExonProbesetLocationHg19,
hugene10stprobeset.db,
hugene10sttranscriptcluster.db,
hugene10stv1probe,
hugene11stprobeset.db,
hugene11sttranscriptcluster.db,
human.db0,
HuO22.db,
hwgcod.db,
illuminaHumanDASLBeadID.db,
IlluminaHumanMethylation27k.db,
illuminaHumanv1.db,
illuminaHumanv1BeadID.db,
illuminaHumanv2.db,
illuminaHumanv2BeadID.db,
illuminaHumanv3.db,
illuminaHumanv3BeadID.db,
illuminaHumanv4.db,
illuminaHumanv4BeadID.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,
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,
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,
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,
chicken.db,
chicken.db0,
chimp.db0,
ChromHeatMap,
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,
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,
illuminaHumanv1.db,
illuminaHumanv1BeadID.db,
illuminaHumanv2.db,
illuminaHumanv2BeadID.db,
illuminaHumanv3.db,
illuminaHumanv3BeadID.db,
illuminaHumanv4.db,
illuminaHumanv4BeadID.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,
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,
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,
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
Version
1.12.1
Since
Bioconductor 2.1 (R-2.6)
Package Downloads