API for OrganismDbi
Software to enable the smooth interfacing of different database packages
| Global functions | |
|---|---|
| .bfs | Source code |
| .biocAnnPackages | Source code |
| .byToKeytype | Source code |
| .cantFindResourceMsg | Source code |
| .cds | Source code |
| .cdsBy | Source code |
| .cols | Source code |
| .colsByNodes | Source code |
| .combineMetadata | Source code |
| .compressMetadata | Source code |
| .dbconn | Source code |
| .dbfile | Source code |
| .exons | Source code |
| .exonsBy | Source code |
| .extractDbFiles | Source code |
| .extractPkgsAndCols | Source code |
| .genes | Source code |
| .gentlyExtractDbFiles | Source code |
| .getColsByNodes | Source code |
| .getDbNameFKeys | Source code |
| .getDbObjNames | Source code |
| .getDbObjs | Source code |
| .getForeignKeys | Source code |
| .getKeyRowWithOrgDbAndTxDb | Source code |
| .getMaxEns | Source code |
| .getMetaDataValue | Source code |
| .getOrgDbByClass | Source code |
| .getRelevantSubgraph | Source code |
| .getSelects | Source code |
| .getTxDb | Source code |
| .getTxDbByClass | Source code |
| .hasSynonymousKeys | Source code |
| .keys | Source code |
| .keytypes | Source code |
| .loadOrganismDbiPkg | Source code |
| .lookupDbFromKeytype | Source code |
| .lookupDbNameFromKeytype | Source code |
| .makeReal | Source code |
| .makekeytypeMapping | Source code |
| .mergeSelectResults | Source code |
| .mkeys | Source code |
| .mungeGraphData | Source code |
| .packageTaxIds | Source code |
| .parseCol | Source code |
| .resources | Source code |
| .safelyGetTxDb | Source code |
| .select | Source code |
| .selectByRanges | Source code |
| .selectRangesById | Source code |
| .showGODb | Source code |
| .showGeneralSubObject | Source code |
| .showOrgDb | Source code |
| .showOrganismDbSpecificItems | Source code |
| .showTxDb | Source code |
| .taxIdToOrgDb | Source code |
| .taxIdToOrgDbName | Source code |
| .taxonomyId | Source code |
| .test | Source code |
| .testGraphData | Source code |
| .testKeys | Source code |
| .transcripts | Source code |
| .transcriptsBy | Source code |
| .updateTxDb | Source code |
| .updateTxDbSeqMultiDb | Source code |
| MultiDb | Man page Source code |
| MultiDb-class | Man page |
| OrganismDb | Man page Source code |
| OrganismDb-class | Man page |
| TxDb | Man page |
| TxDb,OrganismDb-method | Man page |
| TxDb<- | Man page |
| TxDb<-,OrganismDb-method | Man page |
| asBED,MultiDb-method | Man page |
| asGFF,MultiDb-method | Man page |
| available.GTFsForTxDbs | Source code |
| cds,MultiDb-method | Man page |
| cdsBy,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 |
| exons,MultiDb-method | Man page |
| exonsBy,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 |
| makeHubGTFIntoTxDb | Source code |
| makeOrganismDbFromBiomart | Man page Source code |
| makeOrganismDbFromTxDb | Man page Source code |
| makeOrganismDbFromUCSC | Man page Source code |
| makeOrganismPackage | Man page Source code |
| makeOuterMcolFromInnerMcol | Source code |
| mapIds,MultiDb-method | Man page |
| mapToTranscripts,ANY,MultiDb-method | Man page |
| metadata,MultiDb-method | Man page |
| microRNAs,MultiDb-method | Man page |
| promoters,MultiDb-method | Man page |
| resources | Man page |
| resources,MultiDb-method | Man page |
| select,MultiDb-method | Man page |
| selectByRanges | Man page |
| selectByRanges,MultiDb-method | Man page |
| selectRangesById | Man page |
| selectRangesById,MultiDb-method | Man page |
| seqinfo,MultiDb-method | Man page |
| tRNAs,MultiDb-method | Man page |
| taxonomyId,MultiDb-method | Man page |
| threeUTRsByTranscript,MultiDb-method | Man page |
| transcripts,MultiDb-method | Man page |
| transcriptsBy,MultiDb-method | Man page |
