OrganismDbi: Software to enable the smooth interfacing of different database packages

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The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

Author
Marc Carlson, Herve Pages, Martin Morgan, Valerie Obenchain
Date of publication
None
Maintainer
Biocore Data Team <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.16.0

View on Bioconductor

Man pages

coordinate-mapping-method
Map range coordinates between transcripts and genome space
makeOrganismDbFromBiomart
Make a OrganismDb object from annotations available on a...
makeOrganismDbFromTxDb
Make an OrganismDb object from an existing TxDb object.
makeOrganismDbFromUCSC
Make a OrganismDb object from annotations available at the...
makeOrganismPackage
Making OrganismDb packages from annotation packages.
OrganismDb
MultiDb and OrganismDb objects
rangeBasedAccessors
Extract genomic features from an object

Files in this package

OrganismDbi/DESCRIPTION
OrganismDbi/NAMESPACE
OrganismDbi/NEWS
OrganismDbi/R
OrganismDbi/R/AllClasses.R
OrganismDbi/R/AllGenerics.R
OrganismDbi/R/createOrganismPackage.R
OrganismDbi/R/methods-select.R
OrganismDbi/R/methods-transcripts.R
OrganismDbi/R/seqinfo.R
OrganismDbi/R/test_OrganismDbi_package.R
OrganismDbi/build
OrganismDbi/build/vignette.rds
OrganismDbi/inst
OrganismDbi/inst/OrgPkg-template
OrganismDbi/inst/OrgPkg-template/DESCRIPTION
OrganismDbi/inst/OrgPkg-template/NAMESPACE
OrganismDbi/inst/OrgPkg-template/R
OrganismDbi/inst/OrgPkg-template/R/zzz.R
OrganismDbi/inst/OrgPkg-template/man
OrganismDbi/inst/OrgPkg-template/man/@PKGNAME@.Rd
OrganismDbi/inst/doc
OrganismDbi/inst/doc/OrganismDbi.R
OrganismDbi/inst/doc/OrganismDbi.Rnw
OrganismDbi/inst/doc/OrganismDbi.pdf
OrganismDbi/inst/extdata
OrganismDbi/inst/extdata/myTxDb.sqlite
OrganismDbi/inst/script
OrganismDbi/inst/script/makeOrgDbPkgs.R
OrganismDbi/inst/script/test_PkgFreeExamples.R
OrganismDbi/inst/unitTests
OrganismDbi/inst/unitTests/test_construction.R
OrganismDbi/inst/unitTests/test_mapIds.R
OrganismDbi/inst/unitTests/test_select.R
OrganismDbi/inst/unitTests/test_transcripts.R
OrganismDbi/inst/unitTests/test_wrappedFuns.R
OrganismDbi/man
OrganismDbi/man/OrganismDb.Rd
OrganismDbi/man/coordinate-mapping-method.Rd
OrganismDbi/man/makeOrganismDbFromBiomart.Rd
OrganismDbi/man/makeOrganismDbFromTxDb.Rd
OrganismDbi/man/makeOrganismDbFromUCSC.Rd
OrganismDbi/man/makeOrganismPackage.Rd
OrganismDbi/man/rangeBasedAccessors.Rd
OrganismDbi/tests
OrganismDbi/tests/OrganismDbi_unit_tests.R
OrganismDbi/vignettes
OrganismDbi/vignettes/OrganismDbi.Rnw
OrganismDbi/vignettes/databaseTypes.pdf