Make RATs more friendly towards Bioconductor by allowing users to supply their annotation in established Bioconductor formats, such as GRanges or TxDb. Either format should be simple to convert to a list of transcript and gene IDs, but currently users have to do this themselves. If we aim to submit RATs to Bioconductor, RATs should become compatible with the Bioconductor structures directly.

• helper function(s) to create transcript-to-gene look-up table from a TxDb or from a GRanges representation of a GTF/GFF3.

• Convert the internal GTF parser to rely on rtracklayer and GenomicRanges?

• Granges would be useful for plotting gene models (see Plot gene models #44)