i'm interested in building a table of counts from BAM files produced by a PE RNA-seq experiment, for RepeatMasker annotations. essentially to know how many RNA-seq reads map to a particular LTR, etc. i've searched for those annotations among the Bioconductor annotation packages but couldn't find anything with the keyword repeat. searching on the support site led me to this Rsubread::featureCounts extremely slow on some annotations on the performance of featureCounts for that purpose but it has no details about how the annotations are input to the software. i'm familiar with using 'summarizeOverlaps()' from the GenomicAlignments package to build a table of counts from gene annotations, which i find it convenient because the input is a 'TxDb' object and the output is a 'SummarizedExperiment' object. any hint about how to do this in Bioconductor will be very appreciated.