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| as.list-method | TranscriptDb objects |
| cds | Extract genomic features from an object |
| cds-method | Extract genomic features from an object |
| cdsBy | Extract and group genomic features of a given type |
| cdsBy-method | Extract and group genomic features of a given type |
| cdsByOverlaps | Extract genomic features from an object based on their by genomic location |
| cdsByOverlaps-method | Extract genomic features from an object based on their by genomic location |
| class:FeatureDb | TranscriptDb objects |
| class:TranscriptDb | TranscriptDb objects |
| cols-method | TranscriptDb objects |
| DEFAULT_CIRC_SEQS | character vector: strings that are usually circular chromosomes |
| exons | Extract genomic features from an object |
| exons-method | Extract genomic features from an object |
| exonsBy | Extract and group genomic features of a given type |
| exonsBy-method | Extract and group genomic features of a given type |
| exonsByOverlaps | Extract genomic features from an object based on their by genomic location |
| exonsByOverlaps-method | Extract genomic features from an object based on their by genomic location |
| exons_deprecated | Functions that compute genomic regions of interest. |
| extractTranscripts | Tools for extracting transcript sequences |
| extractTranscriptsFromGenome | Tools for extracting transcript sequences |
| FeatureDb | TranscriptDb objects |
| FeatureDb-class | TranscriptDb objects |
| features | Extract simple features from a FeatureDb object |
| features-method | Extract simple features from a FeatureDb object |
| fiveUTRsByTranscript | Extract and group genomic features of a given type |
| fiveUTRsByTranscript-method | Extract and group genomic features of a given type |
| getChromInfoFromBiomart | Making a TranscriptDb object from annotations available on a BioMart database |
| getChromInfoFromUCSC | Making a TranscriptDb object from annotations available at the UCSC Genome Browser |
| id2name | Map internal ids to external names for a given feature type |
| intronsByTranscript | Extract and group genomic features of a given type |
| intronsByTranscript-method | Extract and group genomic features of a given type |
| introns_deprecated | Functions that compute genomic regions of interest. |
| isActiveSeq | TranscriptDb objects |
| isActiveSeq-method | TranscriptDb objects |
| isActiveSeq<- | TranscriptDb objects |
| isActiveSeq<--method | TranscriptDb objects |
| keys-method | TranscriptDb objects |
| keytypes-method | TranscriptDb objects |
| loadFeatures | Methods to save and load the database contents for a Transcript Object. |
| makeFeatureDbFromUCSC | Making a FeatureDb object from annotations available at the UCSC Genome Browser |
| makeTranscriptDb | Making a TranscriptDb object from user supplied annotations |
| makeTranscriptDbFromBiomart | Making a TranscriptDb object from annotations available on a BioMart database |
| makeTranscriptDbFromUCSC | Making a TranscriptDb object from annotations available at the UCSC Genome Browser |
| makeTxDbPackage | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
| makeTxDbPackageFromBiomart | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
| makeTxDbPackageFromUCSC | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
| metadata-method | TranscriptDb objects |
| saveFeatures | Methods to save and load the database contents for a Transcript Object. |
| saveFeatures-method | Methods to save and load the database contents for a Transcript Object. |
| select-method | TranscriptDb objects |
| seqinfo-method | TranscriptDb objects |
| show-method | TranscriptDb objects |
| supportedUCSCFeatureDbTables | Making a FeatureDb object from annotations available at the UCSC Genome Browser |
| supportedUCSCFeatureDbTracks | Making a FeatureDb object from annotations available at the UCSC Genome Browser |
| supportedUCSCtables | Making a TranscriptDb object from annotations available at the UCSC Genome Browser |
| threeUTRsByTranscript | Extract and group genomic features of a given type |
| threeUTRsByTranscript-method | Extract and group genomic features of a given type |
| TranscriptDb | TranscriptDb objects |
| TranscriptDb-class | TranscriptDb objects |
| transcriptLocs2refLocs | Tools for extracting transcript sequences |
| transcripts | Extract genomic features from an object |
| transcripts-method | Extract genomic features from an object |
| transcriptsBy | Extract and group genomic features of a given type |
| transcriptsBy-method | Extract and group genomic features of a given type |
| transcriptsByOverlaps | Extract genomic features from an object based on their by genomic location |
| transcriptsByOverlaps-method | Extract genomic features from an object based on their by genomic location |
| transcripts_deprecated | Functions that compute genomic regions of interest. |
| transcriptWidths | Tools for extracting transcript sequences |
| UCSCFeatureDbTableSchema | Making a FeatureDb object from annotations available at the UCSC Genome Browser |