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I have an automated annotation output (AUGUSTUS) to curate, for instance splitting genes that were artificially fused. I am searching for tools using Bioconductor that could for instance split all transcripts in a TxDb that overlap with a given GRanges object, and relabel their exons and CDS smartly, or add new UTRs to a TxDb object, etc. Is there a package somewhere that already does that?
I think you can find those transcripts not overlapping with a GRanges object easily via ?GenomicRanges::setdiff, but I don't know how to annotate them easily and smartly. Perhaps with plyranges?