The best pacakge to annotate a set of regions

Question

[changxu.fan]

Looking for recommendations here~ I have a set of transcription start sites (TSS) called from a nanoCAGE experiment, in bed format. I'm trying to assess the quality of this experiment through the distribution of the called TSS sites in the genome, especially with respect to genes (5'UTR, exon, intron and 3'UTR). The expectation is that these sites (i.e. all the regions in the bed file) should concentrate at 5'UTR of the genes. Is there a good package in R to do it?

Thanks in advance!