DEFAULT_CIRC_SEQS       character vector: strings that are usually
                        circular chromosomes
FeatureDb-class         FeatureDb objects
TxDb-class              TxDb objects
asBED,TxDb-method       Coerce to file format structures
extractTranscriptSeqs   Extract transcript sequences from chromosomes
extractUpstreamSeqs     Extract sequences upstream of a set of genes or
                        transcripts
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
makeTxDb                Making a TxDb object from user supplied
                        annotations
makeTxDbFromBiomart     Make a TxDb object from annotations available
                        on a BioMart database
makeTxDbFromGFF         Make a TxDb object from annotations available
                        as a GFF3 or GTF file
makeTxDbFromGRanges     Make a TxDb object from a GRanges object
makeTxDbFromUCSC        Make a TxDb object from annotations available
                        at the UCSC Genome Browser
makeTxDbPackage         Making a TxDb package from annotations
                        available at the UCSC Genome Browser, biomaRt
                        or from another source.
mapToTranscripts        Map range coordinates between transcripts and
                        genome space
nearest-methods         Finding the nearest genomic range neighbor in a
                        TxDb
select-methods          Using the "select" interface on TxDb objects
sortExonsByRank         Sort exons by rank
transcriptLengths       Extract the transcript lengths from a TxDb
                        object
transcriptLocs2refLocs
                        Converting transcript-based locations into
                        reference-based locations
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
