Software to enable the smooth interfacing of different database
packages
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Documentation for package ‘OrganismDbi’ version 1.40.0
Help Pages
| asBED-method | Extract genomic features from an object |
| asGFF-method | Extract genomic features from an object |
| cds-method | Extract genomic features from an object |
| cdsBy-method | Extract genomic features from an object |
| class:MultiDb | MultiDb and OrganismDb objects |
| class:OrganismDb | MultiDb and OrganismDb objects |
| columns-method | MultiDb and OrganismDb objects |
| dbconn-method | MultiDb and OrganismDb objects |
| dbfile-method | MultiDb and OrganismDb objects |
| distance-method | Extract genomic features from an object |
| exons-method | Extract genomic features from an object |
| exonsBy-method | Extract genomic features from an object |
| extractTranscriptSeqs-method | Extract genomic features from an object |
| extractUpstreamSeqs-method | Extract genomic features from an object |
| fiveUTRsByTranscript-method | Extract genomic features from an object |
| genes-method | Extract genomic features from an object |
| getTxDbIfAvailable | Extract genomic features from an object |
| getTxDbIfAvailable-method | Extract genomic features from an object |
| intronsByTranscript-method | Extract genomic features from an object |
| isActiveSeq-method | Extract genomic features from an object |
| isActiveSeq<--method | Extract genomic features from an object |
| keys-method | MultiDb and OrganismDb objects |
| keytypes-method | MultiDb and OrganismDb objects |
| makeOrganismDbFromBiomart | Make a OrganismDb object from annotations available on a BioMart database |
| makeOrganismDbFromTxDb | Make an OrganismDb object from an existing TxDb object. |
| makeOrganismDbFromUCSC | Make a OrganismDb object from annotations available at the UCSC Genome Browser |
| makeOrganismPackage | Making OrganismDb packages from annotation packages. |
| mapIds-method | MultiDb and OrganismDb objects |
| mapToTranscripts-method | Map range coordinates between transcripts and genome space |
| metadata-method | MultiDb and OrganismDb objects |
| microRNAs-method | Extract genomic features from an object |
| MultiDb | MultiDb and OrganismDb objects |
| MultiDb-class | MultiDb and OrganismDb objects |
| OrganismDb | MultiDb and OrganismDb objects |
| OrganismDb-class | MultiDb and OrganismDb objects |
| promoters-method | Extract genomic features from an object |
| resources | MultiDb and OrganismDb objects |
| resources-method | MultiDb and OrganismDb objects |
| select-method | MultiDb and OrganismDb objects |
| selectByRanges | MultiDb and OrganismDb objects |
| selectByRanges-method | MultiDb and OrganismDb objects |
| selectRangesById | MultiDb and OrganismDb objects |
| selectRangesById-method | MultiDb and OrganismDb objects |
| seqinfo-method | MultiDb and OrganismDb objects |
| taxonomyId-method | MultiDb and OrganismDb objects |
| threeUTRsByTranscript-method | Extract genomic features from an object |
| transcripts-method | Extract genomic features from an object |
| transcriptsBy-method | Extract genomic features from an object |
| tRNAs-method | Extract genomic features from an object |
| TxDb | MultiDb and OrganismDb objects |
| TxDb-method | MultiDb and OrganismDb objects |
| TxDb<- | MultiDb and OrganismDb objects |
| TxDb<--method | MultiDb and OrganismDb objects |