AnnotationDbi: Annotation Database Interface

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

AuthorHervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.36.1

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

Files in this package

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

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