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| as.list-method | TranscriptDb objects |
| asBED-method | Coerce to file format structures |
| asGFF-method | Coerce to file format structures |
| 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 | FeatureDb objects |
| class:TranscriptDb | TranscriptDb objects |
| columns-method | Using the "select" interface on TranscriptDb objects |
| DEFAULT_CIRC_SEQS | character vector: strings that are usually circular chromosomes |
| determineDefaultSeqnameStyle | Deprecated Functions in package 'GenomicFeatures' |
| determineDefaultSeqnameStyle-method | Deprecated Functions in package 'GenomicFeatures' |
| disjointExons | Extract genomic features from an object |
| disjointExons-method | Extract genomic features from an object |
| distance-method | Finding the nearest genomic range neighbor in a TranscriptDb |
| 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 | Various OBSOLETE tools for extracting transcript sequences |
| extractTranscriptSeqs | Extract transcript sequences from chromosomes |
| extractTranscriptSeqs-method | Extract transcript sequences from chromosomes |
| extractTranscriptsFromGenome | Various OBSOLETE tools for extracting transcript sequences |
| FeatureDb | FeatureDb objects |
| FeatureDb-class | FeatureDb 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 |
| genes | Extract genomic features from an object |
| genes-method | Extract genomic features from an object |
| GenomicFeatures-deprecated | Deprecated Functions in package 'GenomicFeatures' |
| getChromInfoFromBiomart | Make a TranscriptDb object from annotations available on a BioMart database |
| getChromInfoFromUCSC | Make a TranscriptDb object from annotations available at the UCSC Genome Browser |
| getPromoterSeq | Get gene promoter sequences |
| getPromoterSeq-method | Get gene promoter sequences |
| 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 | Using the "select" interface on TranscriptDb objects |
| keytypes-method | Using the "select" interface on TranscriptDb objects |
| loadFeatures | Methods to save and load the database contents for a TranscriptDb or FeatureDb object. |
| makeFDbPackageFromUCSC | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
| makeFeatureDbFromUCSC | Making a FeatureDb object from annotations available at the UCSC Genome Browser |
| makeTranscriptDb | Making a TranscriptDb object from user supplied annotations |
| makeTranscriptDbFromBiomart | Make a TranscriptDb object from annotations available on a BioMart database |
| makeTranscriptDbFromGFF | Make a TranscriptDb object from annotations available as a GFF3 or GTF file |
| makeTranscriptDbFromUCSC | Make 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. |
| microRNAs | Extract genomic features from an object |
| microRNAs-method | Extract genomic features from an object |
| nearest-methods | Finding the nearest genomic range neighbor in a TranscriptDb |
| promoters-method | Extract genomic features from an object |
| saveFeatures | Methods to save and load the database contents for a TranscriptDb or FeatureDb object. |
| saveFeatures-method | Methods to save and load the database contents for a TranscriptDb or FeatureDb object. |
| select-method | Using the "select" interface on TranscriptDb objects |
| select-methods | Using the "select" interface on TranscriptDb objects |
| seqinfo-method | TranscriptDb objects |
| seqinfo<--method | TranscriptDb objects |
| sortExonsByRank | Various OBSOLETE tools for extracting transcript sequences |
| supportedMiRBaseBuildValues | Making a TranscriptDb packages from annotations available at the UCSC Genome Browser, biomaRt or from another source. |
| 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 | Make 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 | Various OBSOLETE 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 | Various OBSOLETE tools for extracting transcript sequences |
| tRNAs | Extract genomic features from an object |
| tRNAs-method | Extract genomic features from an object |
| UCSCFeatureDbTableSchema | Making a FeatureDb object from annotations available at the UCSC Genome Browser |