DEFAULT_CIRC_SEQS       character vector: strings that are usually
                        circular chromosomes
FeatureDb-class         FeatureDb objects
GenomicFeatures-deprecated
                        Deprecated Functions in package
                        'GenomicFeatures'
TranscriptDb-class      TranscriptDb objects
asBED,TranscriptDb-method
                        Coerce to file format structures
extractTranscriptSeqs   Extract transcript sequences from chromosomes
extractTranscriptsFromGenome
                        Various OBSOLETE tools for extracting
                        transcript sequences
features                Extract simple features from a FeatureDb object
getPromoterSeq          Get gene promoter sequences
id2name                 Map internal ids to external names for a given
                        feature type
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.
nearest-methods         Finding the nearest genomic range neighbor in a
                        TranscriptDb
saveFeatures            Methods to save and load the database contents
                        for a TranscriptDb or FeatureDb object.
select-methods          Using the "select" interface on TranscriptDb
                        objects
transcripts             Extract genomic features from an object
transcriptsBy           Extract and group genomic features of a given
                        type
transcriptsByOverlaps   Extract genomic features from an object based
                        on their by genomic location
transcripts_deprecated
                        Functions that compute genomic regions of
                        interest.
