character vector: strings that are usually circular chromosomes
FeatureDb objects
TxDb objects
Coerce to file format structures
Map range coordinates between transcripts and genome space
Compute coverage by transcript (or CDS) of a set of ranges
Extract non-overlapping exon parts from an object
Extract transcript (or CDS) sequences from chromosome sequences
Extract sequences upstream of a set of genes or transcripts
Extract simple features from a FeatureDb object
Get gene promoter sequences
Map internal ids to external names for a given feature type
Making a FeatureDb object from annotations available at the UCSC Genome Browser
Making a TxDb object from user supplied annotations
Make a TxDb object from annotations available on a BioMart database
Make a TxDb object from annotations available as a GFF3 or GTF file
Make a TxDb object from a GRanges object
Make a TxDb object from annotations available at the UCSC Genome Browser
Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.
Extract microRNA or tRNA genomic ranges from an object
Finding the nearest genomic range neighbor in a TxDb
Using the "select" interface on TxDb objects
Extract the transcript lengths from a TxDb object
Converting transcript-based locations into reference-based locations
Extract genomic features from an object
Extract and group genomic features of a given type
Extract genomic features from an object based on their by genomic location