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

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.

AuthorMarc Carlson, Herve Pages, Martin Morgan, Valerie Obenchain
Date of publicationNone
MaintainerBiocore Data Team <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.16.0

View on Bioconductor

Functions

asBED,MultiDb-method Man page
asGFF,MultiDb-method Man page
cdsBy,MultiDb-method Man page
cds,MultiDb-method Man page
class:MultiDb Man page
class:OrganismDb Man page
columns,MultiDb-method Man page
dbconn,MultiDb-method Man page
dbfile,MultiDb-method Man page
disjointExons,MultiDb-method Man page
distance,GenomicRanges,MultiDb-method Man page
exonsBy,MultiDb-method Man page
exons,MultiDb-method Man page
extractTranscriptSeqs,BSgenome-method Man page
extractUpstreamSeqs,MultiDb-method Man page
fiveUTRsByTranscript,MultiDb-method Man page
genes,MultiDb-method Man page
getTxDbIfAvailable Man page
getTxDbIfAvailable,MultiDb-method Man page
intronsByTranscript,MultiDb-method Man page
isActiveSeq<-,MultiDb-method Man page
isActiveSeq,MultiDb-method Man page
keys,MultiDb-method Man page
keytypes,MultiDb-method Man page
makeOrganismDbFromBiomart Man page
makeOrganismDbFromTxDb Man page
makeOrganismDbFromUCSC Man page
makeOrganismPackage Man page
mapIds,MultiDb-method Man page
mapToTranscripts,ANY,MultiDb-method Man page
metadata,MultiDb-method Man page
microRNAs,MultiDb-method Man page
MultiDb Man page
MultiDb-class Man page
OrganismDb Man page
OrganismDb-class Man page
promoters,MultiDb-method Man page
resources Man page
resources,MultiDb-method Man page
selectByRanges Man page
selectByRanges,MultiDb-method Man page
select,MultiDb-method Man page
selectRangesById Man page
selectRangesById,MultiDb-method Man page
seqinfo,MultiDb-method Man page
taxonomyId,MultiDb-method Man page
threeUTRsByTranscript,MultiDb-method Man page
transcriptsBy,MultiDb-method Man page
transcripts,MultiDb-method Man page
tRNAs,MultiDb-method Man page
TxDb Man page
TxDb<- Man page
TxDb<-,OrganismDb-method Man page
TxDb,OrganismDb-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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