Package: OrganismDbi 1.54.0

Bioconductor Package Maintainer

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.

Authors:Marc Carlson [aut], Martin Morgan [aut], Valerie Obenchain [aut], Aliyu Atiku Mustapha [ctb], Bioconductor Package Maintainer [cre]

OrganismDbi_1.54.0.tar.gz
OrganismDbi_1.54.0.zip(r-4.7)OrganismDbi_1.54.0.zip(r-4.6)OrganismDbi_1.54.0.zip(r-4.5)
OrganismDbi_1.54.0.tgz(r-4.6-any)OrganismDbi_1.54.0.tgz(r-4.5-any)
OrganismDbi_1.54.0.tar.gz(r-4.7-any)OrganismDbi_1.54.0.tar.gz(r-4.6-any)
OrganismDbi_1.54.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OrganismDbi/json (API)
NEWS

# Install 'OrganismDbi' in R:
install.packages('OrganismDbi', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:OrganismDbi-1.55.1(bioc 3.24)OrganismDbi-1.54.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

annotationinfrastructure

7.07 score 36 packages 54 scripts 39 exports 69 dependencies

Last updated from:3f6b0d3245 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR449
linux-devel-x86_64NOTE925
source / vignettesOK631
linux-release-x86_64NOTE1059
macos-release-arm64NOTE944
macos-oldrel-arm64NOTE1061
windows-develNOTE1339
windows-releaseNOTE845
windows-oldrelNOTE886
wasm-releaseOK369

Exports:asBEDasGFFcdscdsBycolumnsdbconndbfiledistanceexonsexonsByextractUpstreamSeqsfiveUTRsByTranscriptgenesgetTxDbIfAvailableintronsByTranscriptisActiveSeqisActiveSeq<-keyskeytypesmakeOrganismDbFromBiomartmakeOrganismDbFromTxDbmakeOrganismDbFromUCSCmakeOrganismPackagemapIdsmapToTranscriptsmetadatapromotersresourcesselectselectByRangesselectRangesByIdseqinfotaxonomyIdthreeUTRsByTranscripttranscriptstranscriptsBytRNAsTxDbTxDb<-

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RBGLRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysvctrsXMLXVectoryaml

OrganismDbi: A meta framework for Annotation Packages

Marc Carlson, Aliyu Atiku Mustapha

Rendered fromOrganismDbi.Rmdusingknitr::rmarkdownon Jun 17 2026.

Last update: 2023-04-18
Started: 2023-04-18

Readme and manuals

Help Manual

Help pageTopics
Make a OrganismDb object from annotations available on a BioMart databasemakeOrganismDbFromBiomart
Make an OrganismDb object from an existing TxDb object.makeOrganismDbFromTxDb
Make a OrganismDb object from annotations available at the UCSC Genome BrowsermakeOrganismDbFromUCSC
Making OrganismDb packages from annotation packages.makeOrganismPackage
Map range coordinates between transcripts and genome spacemapToTranscripts mapToTranscripts,ANY,MultiDb-method
MultiDb and OrganismDb objectsclass:MultiDb class:OrganismDb columns,MultiDb-method dbconn,MultiDb-method dbfile,MultiDb-method keys,MultiDb-method keytypes,MultiDb-method mapIds,MultiDb-method metadata,MultiDb-method MultiDb MultiDb-class OrganismDb OrganismDb-class resources resources,MultiDb-method select,MultiDb-method selectByRanges selectByRanges,MultiDb-method selectRangesById selectRangesById,MultiDb-method seqinfo,MultiDb-method taxonomyId,MultiDb-method TxDb TxDb,OrganismDb-method TxDb<- TxDb<-,OrganismDb-method
Extract genomic features from an objectasBED,MultiDb-method asGFF,MultiDb-method cds,MultiDb-method cdsBy,MultiDb-method distance,GenomicRanges,MultiDb-method exons,MultiDb-method exonsBy,MultiDb-method extractTranscriptSeqs,BSgenome-method extractUpstreamSeqs,MultiDb-method fiveUTRsByTranscript,MultiDb-method genes,MultiDb-method getTxDbIfAvailable getTxDbIfAvailable,MultiDb-method intronsByTranscript,MultiDb-method isActiveSeq,MultiDb-method isActiveSeq<-,MultiDb-method promoters,MultiDb-method threeUTRsByTranscript,MultiDb-method transcripts,MultiDb-method transcriptsBy,MultiDb-method tRNAs,MultiDb-method