AnnotationDbi: Annotation Database Interface

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AnnotationDbi")
AuthorHervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li
Bioconductor views Annotation GenomeAnnotation Microarray Sequencing
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.36.2

View on Bioconductor

Man pages

AnnDbObj-class: AnnDbObj objects

AnnDbPkg-checker: Check the SQL data contained in an SQLite-based annotation...

AnnotationDb-class: AnnotationDb objects and their progeny, methods etc.

AnnotationDbi-internals: AnnotationDbi internals

Bimap: Bimap objects and the Bimap interface

Bimap-direction: Methods for getting/setting the direction of a Bimap object,...

Bimap-envirAPI: Environment-like API for Bimap objects

BimapFiltering: Methods for getting/setting the filters on a Bimap object

BimapFormatting: Formatting a Bimap as a list or character vector

Bimap-keys: Methods for manipulating the keys of a Bimap object

Bimap-toTable: Methods for manipulating a Bimap object in a data-frame style

colsAndKeytypes: Descriptions of available values for 'columns' and...

createSimpleBimap: Creates a simple Bimap from a SQLite database in an situation...

GOColsAndKeytypes: Descriptions of available values for 'columns' and 'keytypes'...

GOFrame: GOFrame and GOAllFrame objects

GOTerms-class: Class "GOTerms"

InparanoidColsAndKeytypes: Descriptions of available values for 'columns' and 'keytypes'...

inpIDMapper: Convenience functions for mapping IDs through an appropriate...

KEGGFrame: KEGGFrame objects

make_eg_to_go_map: Create GO to Entrez Gene maps for chip-based packages

makeGOGraph: A convenience function to generate graphs based on the GO.db...

print.probetable: Print method for probetable objects

toSQLStringSet: Convert a vector to a quoted string for use as a SQL value...

unlist2: A replacement for unlist() that does not mangle the names

Functions

ACCNUM Man page
ACYRTHOSIPHON_PISUM Man page
AEDES_AEGYPTI Man page
AgiAnnDbMap Man page
AgiAnnDbMap-class Man page
ALIAS Man page
AnnDbBimap Man page
AnnDbBimap-class Man page
AnnDbMap Man page
AnnDbMap-class Man page
AnnDbObj Man page
AnnDbObj-class Man page
AnnDbObj-objects Man page
AnnDbPkg-checker Man page
AnnObj Man page
AnnObj-class Man page
AnnotationDb Man page
AnnotationDb-class Man page
ANOPHELES_GAMBIAE Man page
APIS_MELLIFERA Man page
ARABIDOPSIS_THALIANA Man page
ARACYC Man page
ARACYCENZYME Man page
as.character,AnnDbBimap-method Man page
as.character,FlatBimap-method Man page
as.data.frame,Bimap-method Man page
as.list Man page
as.list,AgiAnnDbMap-method Man page
as.list,Bimap-method Man page
as.list,FlatBimap-method Man page
as.list,GoAnnDbBimap-method Man page
as.list,GOTermsAnnDbBimap-method Man page
as.list,IpiAnnDbMap-method Man page
ASPERGILLUS_FUMIGATUS Man page
BATRACHOCHYTRIUM_DENDROBATIDIS Man page
Bimap Man page
Bimap-class Man page
Bimap-direction Man page
Bimap-envirAPI Man page
BimapFormatting Man page
Bimap-keys Man page
[,Bimap-method Man page
[[,Bimap-method Man page
$,Bimap-method Man page
Bimap-toTable Man page
BOMBYX_MORI Man page
BOS_TAURUS Man page
BRANCHIOSTOMA_FLORIDAE Man page
BRUGIA_MALAYI Man page
CAENORHABDITIS_BRENNERI Man page
CAENORHABDITIS_BRIGGSAE Man page
CAENORHABDITIS_ELEGANS Man page
CAENORHABDITIS_JAPONICA Man page
CAENORHABDITIS_REMANEI Man page
CANDIDA_ALBICANS Man page
CANDIDA_GLABRATA Man page
CANIS_FAMILIARIS Man page
CAPITELLA_SPI Man page
CAVIA_PORCELLUS Man page
checkMAPCOUNTS Man page
ChipDb-class Man page
CHLAMYDOMONAS_REINHARDTII Man page
chooseCentralOrgPkgSymbol Man page
CHR Man page
CHRLOC Man page
CHRLOCEND Man page
CIONA_INTESTINALIS Man page
CIONA_SAVIGNYI Man page
class:AgiAnnDbMap Man page
class:AnnDbBimap Man page
class:AnnDbMap Man page
class:AnnDbObj Man page
class:AnnObj Man page
class:AnnotationDb Man page
class:Bimap Man page
class:FlatBimap Man page
class:Go3AnnDbBimap Man page
class:GOAllFrame Man page
class:GoAnnDbBimap Man page
class:GOFrame Man page
class:GOTerms Man page
class:GOTermsAnnDbBimap Man page
class:IpiAnnDbMap Man page
class:KEGGFrame Man page
class:L2Rlink Man page
class:ProbeAnnDbBimap Man page
class:ProbeAnnDbMap Man page
class:ProbeGo3AnnDbBimap Man page
class:ProbeIpiAnnDbMap Man page
COCCIDIOIDES_IMMITIS Man page
colmetanames Man page
colmetanames,AnnDbBimap-method Man page
colmetanames,FlatBimap-method Man page
colnames Man page
colnames,AnnDbBimap-method Man page
colnames,FlatBimap-method Man page
cols Man page
columns Man page
columns,AnnotationDb-method Man page
columns,ChipDb-method Man page
columns,GODb-method Man page
columns,Inparanoid8Db-method Man page
columns,InparanoidDb-method Man page
columns,OrgDb-method Man page
columns,ReactomeDb-method Man page
COMMON Man page
contents,Bimap-method Man page
COPRINOPSIS_CINEREUS Man page
count.links Man page
count.links,Bimap-method Man page
count.links,Go3AnnDbBimap-method Man page
count.mappedkeys Man page
count.mappedkeys,ANY-method Man page
count.mappedkeys,Bimap-method Man page
count.mappedLkeys Man page
count.mappedLkeys,AgiAnnDbMap-method Man page
count.mappedLkeys,AnnDbBimap-method Man page
count.mappedLkeys,Bimap-method Man page
count.mappedLkeys,Go3AnnDbBimap-method Man page
count.mappedRkeys Man page
count.mappedRkeys,AnnDbBimap-method Man page
count.mappedRkeys,AnnDbMap-method Man page
count.mappedRkeys,Bimap-method Man page
count.mappedRkeys,Go3AnnDbBimap-method Man page
createAnnObjs.SchemaChoice Man page
createSimpleBimap Man page
CRYPTOCOCCUS_NEOFORMANS Man page
CRYPTOSPORIDIUM_HOMINIS Man page
CRYPTOSPORIDIUM_PARVUM Man page
CULEX_PIPIENS Man page
CYANIDIOSCHYZON_MEROLAE Man page
DANIO_RERIO Man page
DAPHNIA_PULEX Man page
dbconn Man page
dbconn,AnnDbObj-method Man page
dbconn,AnnotationDb-method Man page
dbconn,environment-method Man page
dbconn,SQLiteConnection-method Man page
dbfile Man page
dbfile,AnnDbObj-method Man page
dbfile,AnnotationDb-method Man page
dbFileConnect Man page
dbFileDisconnect Man page
dbfile,environment-method Man page
dbfile,SQLiteConnection-method Man page
dbGetTable Man page
dbInfo Man page
dbInfo,AnnDbObj-method Man page
dbInfo,DBIConnection-method Man page
dbInfo,environment-method Man page
dbmeta Man page
dbmeta,AnnDbObj-method Man page
dbmeta,DBIConnection-method Man page
dbmeta,environment-method Man page
dbschema Man page
dbschema,AnnDbObj-method Man page
dbschema,DBIConnection-method Man page
dbschema,environment-method Man page
DEBARYOMYCES_HANSENII Man page
debugSQL Man page
Definition Man page
DEFINITION Man page
Definition,character-method Man page
Definition,GOTermsAnnDbBimap-method Man page
Definition,GOTerms-method Man page
DESCRIPTION Man page
DICTYOSTELIUM_DISCOIDEUM Man page
dim,Bimap-method Man page
direction Man page
direction<- Man page
direction<-,AnnDbBimap-method Man page
direction,AnnDbBimap-method Man page
direction<-,AnnDbMap-method Man page
direction<-,FlatBimap-method Man page
direction,FlatBimap-method Man page
DROSOPHILA_ANANASSAE Man page
DROSOPHILA_GRIMSHAWI Man page
DROSOPHILA_MELANOGASTER Man page
DROSOPHILA_MOJAVENSIS Man page
DROSOPHILA_PSEUDOOBSCURA Man page
DROSOPHILA_VIRILIS Man page
DROSOPHILA_WILLISTONI Man page
eapply Man page
eapply,Bimap-method Man page
ENSEMBL Man page
ENSEMBLPROT Man page
ENSEMBLTRANS Man page
ENTAMOEBA_HISTOLYTICA Man page
ENTREZID Man page
ENZYME Man page
EQUUS_CABALLUS Man page
ESCHERICHIA_COLIK12 Man page
EVIDENCE Man page
EVIDENCEALL Man page
exists Man page
exists,ANY,ANY,Bimap-method Man page
exists,ANY,Bimap,missing-method Man page
exposeAllProbes Man page
exposeAllProbes,AnnDbBimap-method Man page
filterSeeds Man page
FlatBimap Man page
FlatBimap-class Man page
FUSARIUM_GRAMINEARUM Man page
GALLUS_GALLUS Man page
GASTEROSTEUS_ACULEATUS Man page
GENENAME Man page
get Man page
get,ANY,ANY,Bimap-method Man page
get,ANY,Bimap,missing-method Man page
getBimapFilters Man page
getBimapFilters,AnnDbBimap-method Man page
getGOFrameData Man page
getGOFrameData,GOAllFrame-method Man page
getGOFrameData,GOFrame-method Man page
getKEGGFrameData Man page
getKEGGFrameData,KEGGAllFrame-method Man page
getKEGGFrameData,KEGGFrame-method Man page
getOrgPkgForSchema Man page
GIARDIA_LAMBLIA Man page
GO Man page
Go3AnnDbBimap Man page
Go3AnnDbBimap-class Man page
GOALL Man page
GOAllFrame Man page
GOAllFrame-class Man page
GOAllFrame,GOFrame-method Man page
GoAnnDbBimap Man page
GoAnnDbBimap-class Man page
GODb-class Man page
GOFrame Man page
GOFrame-class Man page
GOFrame,data.frame,character-method Man page
GOFrame,data.frame,missing-method Man page
GOID Man page
GOID,character-method Man page
GOID,GOTermsAnnDbBimap-method Man page
GOID,GOTerms-method Man page
GOTerms Man page
GOTermsAnnDbBimap Man page
GOTermsAnnDbBimap-class Man page
GOTerms-class Man page
hasMultiProbes Man page
hasMultiProbes,ProbeAnnDbBimap-method Man page
hasMultiProbes,ProbeAnnDbMap-method Man page
hasMultiProbes,ProbeGo3AnnDbBimap-method Man page
hasMultiProbes,ProbeIpiAnnDbMap-method Man page
hasSingleProbes Man page
hasSingleProbes,ProbeAnnDbBimap-method Man page
hasSingleProbes,ProbeAnnDbMap-method Man page
hasSingleProbes,ProbeGo3AnnDbBimap-method Man page
hasSingleProbes,ProbeIpiAnnDbMap-method Man page
head,FlatBimap-method Man page
HELOBDELLA_ROBUSTA Man page
idConverter Man page
initialize,FlatBimap-method Man page
initialize,GOTerms-method Man page
initialize,L2Rlink-method Man page
InparanoidDb-class Man page
inpIDMapper Man page
INTERPRO Man page
intraIDMapper Man page
IPI Man page
IpiAnnDbMap Man page
IpiAnnDbMap-class Man page
isNA Man page
isNA,ANY-method Man page
isNA,Bimap-method Man page
isNA,environment-method Man page
IXODES_SCAPULARIS Man page
KEGGFrame Man page
KEGGFrame-class Man page
KEGGFrame,data.frame,character-method Man page
KEGGFrame,data.frame,missing-method Man page
keyname Man page
keyname,Bimap-method Man page
keys Man page
keys<- Man page
keys,AnnotationDb-method Man page
keys<-,Bimap-method Man page
keys,Bimap-method Man page
keys,ChipDb-method Man page
keys,GODb-method Man page
keys,Inparanoid8Db-method Man page
keys,InparanoidDb-method Man page
keys,OrgDb-method Man page
keys,ReactomeDb-method Man page
keytypes Man page
keytypes,ChipDb-method Man page
keytypes,GODb-method Man page
keytypes,Inparanoid8Db-method Man page
keytypes,InparanoidDb-method Man page
keytypes,OrgDb-method Man page
keytypes,ReactomeDb-method Man page
KLUYVEROMYCES_LACTIS Man page
L2Rlink Man page
L2Rlink-class Man page
LEISHMANIA_MAJOR Man page
length,Bimap-method Man page
links Man page
links,AnnDbBimap-method Man page
links,Bimap-method Man page
links,FlatBimap-method Man page
links,Go3AnnDbBimap-method Man page
Lkeyname Man page
Lkeyname,AnnDbBimap-method Man page
Lkeyname,Bimap-method Man page
Lkeys Man page
Lkeys<- Man page
Lkeys<-,AnnDbBimap-method Man page
Lkeys,AnnDbBimap-method Man page
Lkeys<-,FlatBimap-method Man page
Lkeys,FlatBimap-method Man page
Lkeys,ProbeAnnDbBimap-method Man page
Lkeys,ProbeAnnDbMap-method Man page
Lkeys,ProbeGo3AnnDbBimap-method Man page
Lkeys,ProbeIpiAnnDbMap-method Man page
Llength Man page
Llength,AnnDbBimap-method Man page
Llength,Bimap-method Man page
Llength,ProbeAnnDbBimap-method Man page
Llength,ProbeAnnDbMap-method Man page
Llength,ProbeGo3AnnDbBimap-method Man page
Llength,ProbeIpiAnnDbMap-method Man page
loadDb Man page
LOTTIA_GIGANTEA Man page
ls Man page
ls,Bimap-method Man page
MACACA_MULATTA Man page
MAGNAPORTHE_GRISEA Man page
make_eg_to_go_map Man page
makeGOGraph Man page
make_go_to_eg_map Man page
MAP Man page
mapIds Man page
mapIds,AnnotationDb-method Man page
mapIds_base Man page
mappedkeys Man page
mappedkeys,Bimap-method Man page
mappedkeys,environment-method Man page
mappedkeys,vector-method Man page
mappedLkeys Man page
mappedLkeys,AgiAnnDbMap-method Man page
mappedLkeys,AnnDbBimap-method Man page
mappedLkeys,FlatBimap-method Man page
mappedLkeys,Go3AnnDbBimap-method Man page
mappedRkeys Man page
mappedRkeys,AnnDbBimap-method Man page
mappedRkeys,AnnDbMap-method Man page
mappedRkeys,FlatBimap-method Man page
mappedRkeys,Go3AnnDbBimap-method Man page
maskMultiProbes Man page
maskMultiProbes,AnnDbBimap-method Man page
maskSingleProbes Man page
maskSingleProbes,AnnDbBimap-method Man page
mergeToNamespaceAndExport Man page
metadata,AnnotationDb-method Man page
mget Man page
mget,ANY,Bimap-method Man page
mget,Bimap-method Man page
MONODELPHIS_DOMESTICA Man page
MONOSIGA_BREVICOLLIS Man page
MUS_MUSCULUS Man page
names,AnnotationDb-method Man page
NASONIA_VITRIPENNIS Man page
NCBICHIP_DB_SeedGenerator Man page
ncol Man page
ncol,Bimap-method Man page
NEMATOSTELLA_VECTENSIS Man page
NEUROSPORA_CRASSA Man page
nhit Man page
nhit,Bimap-method Man page
nhit,environment-method Man page
nhit,list-method Man page
nrow Man page
nrow,AnnDbBimap-method Man page
nrow,AnnDbTable-method Man page
nrow,Bimap-method Man page
nrow,FlatBimap-method Man page
nrow,Go3AnnDbBimap-method Man page
OMIM Man page
Ontology Man page
ONTOLOGY Man page
ONTOLOGYALL Man page
Ontology,character-method Man page
Ontology,GOTermsAnnDbBimap-method Man page
Ontology,GOTerms-method Man page
ORF Man page
OrgDb-class Man page
ORNITHORHYNCHUS_ANATINUS Man page
ORYZA_SATIVA Man page
ORYZIAS_LATIPES Man page
OSTREOCOCCUS_TAURI Man page
PAN_TROGLODYTES Man page
PATH Man page
PEDICULUS_HUMANUS Man page
PFAM Man page
PHYSCOMITRELLA_PATENS Man page
PHYTOPHTHORA_RAMORUM Man page
PHYTOPHTHORA_SOJAE Man page
PLASMODIUM_FALCIPARUM Man page
PLASMODIUM_VIVAX Man page
PMID Man page
PONGO_PYGMAEUS Man page
POPULUS_TRICHOCARPA Man page
print.probetable Man page
PRISTIONCHUS_PACIFICUS Man page
ProbeAnnDbBimap Man page
ProbeAnnDbBimap-class Man page
ProbeAnnDbMap Man page
ProbeAnnDbMap-class Man page
ProbeGo3AnnDbBimap Man page
ProbeGo3AnnDbBimap-class Man page
PROBEID Man page
ProbeIpiAnnDbMap Man page
ProbeIpiAnnDbMap-class Man page
PROSITE Man page
PUCCINIA_GRAMINIS Man page
Rattribnames Man page
Rattribnames<- Man page
Rattribnames<-,AnnDbBimap-method Man page
Rattribnames,AnnDbBimap-method Man page
Rattribnames,Bimap-method Man page
Rattribnames<-,FlatBimap-method Man page
Rattribnames<-,Go3AnnDbBimap-method Man page
RATTUS_NORVEGICUS Man page
ReactomeDb-class Man page
REFSEQ Man page
resort_base Man page
revmap Man page
revmap,AnnDbBimap-method Man page
revmap,Bimap-method Man page
revmap,environment-method Man page
revmap,list-method Man page
RHIZOPUS_ORYZAE Man page
Rkeyname Man page
Rkeyname,AnnDbBimap-method Man page
Rkeyname,Bimap-method Man page
Rkeys Man page
Rkeys<- Man page
Rkeys<-,AnnDbBimap-method Man page
Rkeys,AnnDbBimap-method Man page
Rkeys,AnnDbMap-method Man page
Rkeys<-,FlatBimap-method Man page
Rkeys,FlatBimap-method Man page
Rkeys,Go3AnnDbBimap-method Man page
Rlength Man page
Rlength,AnnDbBimap-method Man page
Rlength,AnnDbMap-method Man page
Rlength,Bimap-method Man page
Rlength,Go3AnnDbBimap-method Man page
SACCHAROMYCES_CEREVISIAE Man page
sample Man page
sample,Bimap-method Man page
sample,environment-method Man page
saveDb Man page
saveDb,AnnotationDb-method Man page
SCHISTOSOMA_MANSONI Man page
SCHIZOSACCHAROMYCES_POMBE Man page
SCLEROTINIA_SCLEROTIORUM Man page
Secondary Man page
Secondary,character-method Man page
Secondary,GOTermsAnnDbBimap-method Man page
Secondary,GOTerms-method Man page
select Man page
select,AnnotationDb-method Man page
select,ChipDb-method Man page
select,GODb-method Man page
select,Inparanoid8Db-method Man page
select,InparanoidDb-method Man page
select,OrgDb-method Man page
select,ReactomeDb-method Man page
setInpBimapFilter Man page
setInpBimapFilter,InpAnnDbBimap-method Man page
SGD Man page
show,AnnDbBimap-method Man page
show,AnnDbTable-method Man page
show,AnnotationDb-method Man page
show,FlatBimap-method Man page
show,GOTerms-method Man page
show,L2Rlink-method Man page
showQCData Man page
SMART Man page
SORGHUM_BICOLOR Man page
species Man page
species,AnnotationDb-method Man page
STAGONOSPORA_NODORUM Man page
STRONGYLOCENTROTUS_PURPURATUS Man page
subset,AnnDbBimap-method Man page
subset,Bimap-method Man page
summary,AnnDbBimap-method Man page
summary,Bimap-method Man page
SYMBOL Man page
Synonym Man page
Synonym,character-method Man page
Synonym,GOTermsAnnDbBimap-method Man page
Synonym,GOTerms-method Man page
tagname Man page
tagname,AnnDbBimap-method Man page
tagname,Bimap-method Man page
tail,FlatBimap-method Man page
TAIR Man page
TAKIFUGU_RUBRIPES Man page
taxonomyId Man page
taxonomyId,AnnotationDb-method Man page
Term Man page
TERM Man page
Term,character-method Man page
Term,GOTermsAnnDbBimap-method Man page
Term,GOTerms-method Man page
testForValidKeytype Man page
testSelectArgs Man page
TETRAHYMENA_THERMOPHILA Man page
TETRAODON_NIGROVIRIDIS Man page
THALASSIOSIRA_PSEUDONANA Man page
THEILERIA_ANNULATA Man page
THEILERIA_PARVA Man page
toggleProbes Man page
toggleProbes,ProbeAnnDbBimap-method Man page
toggleProbes,ProbeAnnDbMap-method Man page
toggleProbes,ProbeGo3AnnDbBimap-method Man page
toggleProbes,ProbeIpiAnnDbMap-method Man page
toSQLStringSet Man page
toTable Man page
toTable,Bimap-method Man page
toTable,FlatBimap-method Man page
TRIBOLIUM_CASTANEUM Man page
TRICHOMONAS_VAGINALIS Man page
TRICHOPLAX_ADHAERENS Man page
TRYPANOSOMA_CRUZI Man page
UNIGENE Man page
UNIPROT Man page
unlist2 Man page
USTILAGO_MAYDIS Man page
XENOPUS_TROPICALIS Man page
YARROWIA_LIPOLYTICA Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/00RTobjs.R R/AllClasses.R R/AllGenerics.R R/AnnDbObj-lowAPI.R R/AnnDbPkg-checker.R R/AnnDbPkg-templates-common.R R/Bimap-envirAPI.R R/Bimap.R R/BimapFormatting.R R/FlatBimap.R R/GOTerms.R R/SQL.R R/createAnnObjs-utils.R R/createAnnObjs.ARABIDOPSISCHIP_DB.R R/createAnnObjs.ARABIDOPSIS_DB.R R/createAnnObjs.COELICOLOR_DB.R R/createAnnObjs.GO_DB.R R/createAnnObjs.INPARANOID_DB.R R/createAnnObjs.KEGG_DB.R R/createAnnObjs.MALARIA_DB.R R/createAnnObjs.NCBICHIP_DBs.R R/createAnnObjs.NCBIORG_DBs.R R/createAnnObjs.ORGANISM_DB.R R/createAnnObjs.PFAM_DB.R R/createAnnObjs.YEASTCHIP_DB.R R/createAnnObjs.YEASTNCBI_DB.R R/createAnnObjs.YEAST_DB.R R/flatten.R R/inpIDMapper.R R/loadDb.R R/makeMap.R R/methods-AnnotationDb.R R/methods-Inparanoid.R R/methods-Inparanoid8.R R/methods-ReactomeDb.R R/methods-SQLiteConnection.R R/methods-geneCentricDbs-keys.R R/methods-geneCentricDbs.R R/print.probetable.R R/test_AnnotationDbi_package.R R/unlist2.R R/utils.R
build
build/vignette.rds
inst
inst/DBschemas
inst/DBschemas/SchemaGuidelines.txt
inst/DBschemas/schemas_0.9
inst/DBschemas/schemas_0.9/00README.TXT
inst/DBschemas/schemas_0.9/ARABIDOPSISCHIP_DB.sql
inst/DBschemas/schemas_0.9/DataTypes.txt
inst/DBschemas/schemas_0.9/FLYCHIP_DB.sql
inst/DBschemas/schemas_0.9/FLY_DB.sql
inst/DBschemas/schemas_0.9/GO_DB.sql
inst/DBschemas/schemas_0.9/HUMANCHIP_DB.sql
inst/DBschemas/schemas_0.9/HUMAN_DB.sql
inst/DBschemas/schemas_0.9/KEGG_DB.sql
inst/DBschemas/schemas_0.9/RODENTCHIP_DB.sql
inst/DBschemas/schemas_0.9/RODENT_DB.sql
inst/DBschemas/schemas_0.9/YEASTCHIP_DB.sql
inst/DBschemas/schemas_0.9/YEAST_DB.sql
inst/DBschemas/schemas_1.0
inst/DBschemas/schemas_1.0/00README.TXT
inst/DBschemas/schemas_1.0/ARABIDOPSISCHIP_DB.sql
inst/DBschemas/schemas_1.0/BOVINECHIP_DB.sql
inst/DBschemas/schemas_1.0/BOVINE_DB.sql
inst/DBschemas/schemas_1.0/CANINECHIP_DB.sql
inst/DBschemas/schemas_1.0/CANINE_DB.sql
inst/DBschemas/schemas_1.0/CHICKENCHIP_DB.sql
inst/DBschemas/schemas_1.0/CHICKEN_DB.sql
inst/DBschemas/schemas_1.0/DataTypes.txt
inst/DBschemas/schemas_1.0/ECOLICHIP_DB.sql
inst/DBschemas/schemas_1.0/ECOLI_DB.sql
inst/DBschemas/schemas_1.0/FLYCHIP_DB.sql
inst/DBschemas/schemas_1.0/FLY_DB.sql
inst/DBschemas/schemas_1.0/GO_DB.sql
inst/DBschemas/schemas_1.0/HUMANCHIP_DB.sql
inst/DBschemas/schemas_1.0/HUMANCROSSCHIP_DB.sql
inst/DBschemas/schemas_1.0/HUMAN_DB.sql
inst/DBschemas/schemas_1.0/INPARANOIDDROME_DB.sql
inst/DBschemas/schemas_1.0/INPARANOIDHOMSA_DB.sql
inst/DBschemas/schemas_1.0/INPARANOIDMUSMU_DB.sql
inst/DBschemas/schemas_1.0/INPARANOIDRATNO_DB.sql
inst/DBschemas/schemas_1.0/INPARANOIDSACCE_DB.sql
inst/DBschemas/schemas_1.0/KEGG_DB.sql
inst/DBschemas/schemas_1.0/MALARIA_DB.sql
inst/DBschemas/schemas_1.0/MOUSECHIP_DB.sql
inst/DBschemas/schemas_1.0/MOUSE_DB.sql
inst/DBschemas/schemas_1.0/PFAM_DB.sql
inst/DBschemas/schemas_1.0/PIGCHIP_DB.sql
inst/DBschemas/schemas_1.0/PIG_DB.sql
inst/DBschemas/schemas_1.0/RATCHIP_DB.sql
inst/DBschemas/schemas_1.0/RAT_DB.sql
inst/DBschemas/schemas_1.0/WORMCHIP_DB.sql
inst/DBschemas/schemas_1.0/WORM_DB.sql
inst/DBschemas/schemas_1.0/YEASTCHIP_DB.sql
inst/DBschemas/schemas_1.0/YEAST_DB.sql
inst/DBschemas/schemas_1.0/ZEBRAFISHCHIP_DB.sql
inst/DBschemas/schemas_1.0/ZEBRAFISH_DB.sql
inst/DBschemas/schemas_2.0
inst/DBschemas/schemas_2.0/00README.TXT
inst/DBschemas/schemas_2.0/ANOPHELES_DB.sql
inst/DBschemas/schemas_2.0/ARABIDOPSISCHIP_DB.sql
inst/DBschemas/schemas_2.0/ARABIDOPSIS_DB.sql
inst/DBschemas/schemas_2.0/BOVINECHIP_DB.sql
inst/DBschemas/schemas_2.0/BOVINE_DB.sql
inst/DBschemas/schemas_2.0/CANINECHIP_DB.sql
inst/DBschemas/schemas_2.0/CANINE_DB.sql
inst/DBschemas/schemas_2.0/CHICKENCHIP_DB.sql
inst/DBschemas/schemas_2.0/CHICKEN_DB.sql
inst/DBschemas/schemas_2.0/CHIMP_DB.sql
inst/DBschemas/schemas_2.0/DataTypes.txt
inst/DBschemas/schemas_2.0/ECOLI_DB.sql
inst/DBschemas/schemas_2.0/FLYCHIP_DB.sql
inst/DBschemas/schemas_2.0/FLY_DB.sql
inst/DBschemas/schemas_2.0/GO_DB.sql
inst/DBschemas/schemas_2.0/HUMANCHIP_DB.sql
inst/DBschemas/schemas_2.0/HUMAN_DB.sql
inst/DBschemas/schemas_2.0/INPARANOID_DB.sql
inst/DBschemas/schemas_2.0/KEGG_DB.sql
inst/DBschemas/schemas_2.0/MALARIA_DB.sql
inst/DBschemas/schemas_2.0/MOUSECHIP_DB.sql
inst/DBschemas/schemas_2.0/MOUSE_DB.sql
inst/DBschemas/schemas_2.0/PFAM_DB.sql
inst/DBschemas/schemas_2.0/PIG_DB.sql
inst/DBschemas/schemas_2.0/RATCHIP_DB.sql
inst/DBschemas/schemas_2.0/RAT_DB.sql
inst/DBschemas/schemas_2.0/RHESUS_DB.sql
inst/DBschemas/schemas_2.0/WORMCHIP_DB.sql
inst/DBschemas/schemas_2.0/WORM_DB.sql
inst/DBschemas/schemas_2.0/XENOPUSCHIP_DB.sql
inst/DBschemas/schemas_2.0/XENOPUS_DB.sql
inst/DBschemas/schemas_2.0/YEASTCHIP_DB.sql
inst/DBschemas/schemas_2.0/YEAST_DB.sql
inst/DBschemas/schemas_2.0/ZEBRAFISHCHIP_DB.sql
inst/DBschemas/schemas_2.0/ZEBRAFISH_DB.sql
inst/DBschemas/schemas_2.1
inst/DBschemas/schemas_2.1/00README.TXT
inst/DBschemas/schemas_2.1/ANOPHELES_DB.sql
inst/DBschemas/schemas_2.1/ARABIDOPSISCHIP_DB.sql
inst/DBschemas/schemas_2.1/ARABIDOPSIS_DB.sql
inst/DBschemas/schemas_2.1/BOVINECHIP_DB.sql
inst/DBschemas/schemas_2.1/BOVINE_DB.sql
inst/DBschemas/schemas_2.1/CANINECHIP_DB.sql
inst/DBschemas/schemas_2.1/CANINE_DB.sql
inst/DBschemas/schemas_2.1/CHICKENCHIP_DB.sql
inst/DBschemas/schemas_2.1/CHICKEN_DB.sql
inst/DBschemas/schemas_2.1/CHIMP_DB.sql
inst/DBschemas/schemas_2.1/COELICOLOR_DB.sql
inst/DBschemas/schemas_2.1/DataTypes.txt
inst/DBschemas/schemas_2.1/ECOLI_DB.sql
inst/DBschemas/schemas_2.1/FLYCHIP_DB.sql
inst/DBschemas/schemas_2.1/FLY_DB.sql
inst/DBschemas/schemas_2.1/GO_DB.sql
inst/DBschemas/schemas_2.1/HUMANCHIP_DB.sql
inst/DBschemas/schemas_2.1/HUMAN_DB.sql
inst/DBschemas/schemas_2.1/INPARANOID_DB.sql
inst/DBschemas/schemas_2.1/KEGG_DB.sql
inst/DBschemas/schemas_2.1/MALARIA_DB.sql
inst/DBschemas/schemas_2.1/MOUSECHIP_DB.sql
inst/DBschemas/schemas_2.1/MOUSE_DB.sql
inst/DBschemas/schemas_2.1/PFAM_DB.sql
inst/DBschemas/schemas_2.1/PIG_DB.sql
inst/DBschemas/schemas_2.1/RATCHIP_DB.sql
inst/DBschemas/schemas_2.1/RAT_DB.sql
inst/DBschemas/schemas_2.1/RHESUS_DB.sql
inst/DBschemas/schemas_2.1/WORMCHIP_DB.sql
inst/DBschemas/schemas_2.1/WORM_DB.sql
inst/DBschemas/schemas_2.1/XENOPUSCHIP_DB.sql
inst/DBschemas/schemas_2.1/XENOPUS_DB.sql
inst/DBschemas/schemas_2.1/YEASTCHIP_DB.sql
inst/DBschemas/schemas_2.1/YEAST_DB.sql
inst/DBschemas/schemas_2.1/ZEBRAFISHCHIP_DB.sql
inst/DBschemas/schemas_2.1/ZEBRAFISH_DB.sql
inst/NOTES-Herve
inst/TODO
inst/doc
inst/doc/AnnotationDbi.R
inst/doc/AnnotationDbi.Rnw
inst/doc/AnnotationDbi.pdf
inst/doc/IntroToAnnotationPackages.R
inst/doc/IntroToAnnotationPackages.Rnw
inst/doc/IntroToAnnotationPackages.pdf
inst/extdata
inst/extdata/HG-U95Av2_probe_tab.gz
inst/extdata/Inp_species_mapping
inst/extdata/hcg110_ID
inst/extdata/hgu95av2_ID
inst/extdata/manyToOneBlackList.Rda
inst/extdata/org.testing.db
inst/extdata/org.testing.db/DESCRIPTION
inst/extdata/org.testing.db/NAMESPACE
inst/extdata/org.testing.db/R
inst/extdata/org.testing.db/R/zzz.R
inst/extdata/org.testing.db/inst
inst/extdata/org.testing.db/inst/extdata
inst/extdata/org.testing.db/inst/extdata/org.testing.sqlite
inst/extdata/org.testing.db/man
inst/extdata/org.testing.db/man/org.TguttataTestingSubset.egBASE.Rd
inst/extdata/org.testing.db/man/org.TguttataTestingSubset.egORGANISM.Rd
inst/extdata/org.testing.db/man/org.TguttataTestingSubset.eg_dbconn.Rd
inst/extdata/resultTable.Rda
inst/script
inst/script/generateMultiCols.R
inst/unitTests
inst/unitTests/test_bimap.R inst/unitTests/test_geneCentricDbs.R inst/unitTests/test_mapIds.R inst/unitTests/test_select.R inst/unitTests/test_select_NOSCHEMA.R inst/unitTests/test_select_inparanoid.R inst/unitTests/test_select_reactome.R
man
man/AnnDbObj-class.Rd man/AnnDbPkg-checker.Rd man/AnnotationDb-class.Rd man/AnnotationDbi-internals.Rd man/Bimap-direction.Rd man/Bimap-envirAPI.Rd man/Bimap-keys.Rd man/Bimap-toTable.Rd man/Bimap.Rd man/BimapFiltering.Rd man/BimapFormatting.Rd man/GOColsAndKeytypes.Rd man/GOFrame.Rd man/GOTerms-class.Rd man/InparanoidColsAndKeytypes.Rd man/KEGGFrame.Rd man/colsAndKeytypes.Rd man/createSimpleBimap.Rd man/inpIDMapper.Rd man/makeGOGraph.Rd man/make_eg_to_go_map.Rd man/print.probetable.Rd man/toSQLStringSet.Rd man/unlist2.Rd
tests
tests/AnnotationDbi_unit_tests.R
vignettes
vignettes/AnnotationDbi.Rnw
vignettes/IntroToAnnotationPackages.Rnw
vignettes/databaseTypes.pdf

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