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 coverageByTranscript Compute coverage by transcript (or CDS) of a set of ranges disjointExons Extract non-overlapping exon parts from an object 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 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 microRNAs Extract microRNA or tRNA genomic ranges from an object nearest-methods Finding the nearest genomic range neighbor in a TxDb select-methods Using the "select" interface on TxDb objects 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