FeatureDb-class         FeatureDb objects
TxDb-class              TxDb objects
asBED,TxDb-method       Coerce to file format structures
coverageByTranscript    Compute coverage by transcript (or CDS) of a
                        set of ranges
exonicParts             Extract non-overlapping exonic or intronic
                        parts from a TxDb-like object
extendExonsIntoIntrons
                        Extend exons by a given number of bases into
                        their adjacent introns
extractTranscriptSeqs   Extract transcript (or CDS) sequences from
                        chromosome sequences
extractUpstreamSeqs     Extract sequences upstream of a set of genes or
                        transcripts
features                Extract simple features from a FeatureDb object
getPromoterSeq          Get gene promoter or terminator sequences
id2name                 Map internal ids to external names for a given
                        feature type
makeFeatureDbFromUCSC   [Moved to txdbmaker] Make a FeatureDb object
                        from annotations available at the UCSC Genome
                        Browser
makeTxDb                [Moved to txdbmaker] Make a TxDb object from
                        user supplied annotations
makeTxDbFromBiomart     [Moved to txdbmaker] Make a TxDb object from
                        annotations available on a BioMart database
makeTxDbFromEnsembl     [Moved to txdbmaker] Make a TxDb object from an
                        Ensembl database
makeTxDbFromGFF         [Moved to txdbmaker] Make a TxDb object from
                        annotations available as a GFF3 or GTF file
makeTxDbFromGRanges     [Moved to txdbmaker] Make a TxDb object from a
                        GRanges object
makeTxDbFromUCSC        [Moved to txdbmaker] Make a TxDb object from
                        annotations available at the UCSC Genome
                        Browser
makeTxDbPackage         [Moved to txdbmaker] Making a TxDb package from
                        annotations available at the UCSC Genome
                        Browser, biomaRt or from another source.
mapIdsToRanges          Map IDs to Genomic Ranges
mapRangesToIds          Map Genomic Ranges to IDs
mapToTranscripts        Map range coordinates between transcripts and
                        genome space
nearest-methods         Finding the nearest genomic range neighbor in a
                        TxDb
proteinToGenome         Map protein-relative coordinates to genomic
                        coordinates
select-methods          Using the "select" interface on TxDb objects
tRNAs                   Extract tRNA genomic ranges from an object
transcriptLengths       Extract the transcript lengths (and other
                        metrics) from a TxDb object
transcriptLocs2refLocs
                        Converting transcript-based locations into
                        reference-based locations
transcripts             Extract genomic features from a TxDb-like
                        object
transcriptsBy           Extract and group genomic features of a given
                        type from a TxDb-like object
transcriptsByOverlaps   Extract genomic features from a TxDb-like
                        object based on their genomic location
