Changelog

Source: NEWS.md

splicelogic 1.1.4

• Added prepare_exons_by_partition() for building input from two sets of transcripts, without needing a estimate column from a DTU analysis.
• Added find_atss() and find_ates() for detecting alternative transcription start and end sites. Both are included in find_all_events().
• Added find_si() (alias find_spliced_introns()), the reverse of find_ri(): an intron that an up transcript splices out but a down transcript retains. find_ri() gains an inverse argument, as find_se() has for find_ie(). Included in find_all_events().
• find_a5ss() and find_a3ss() now label events per moved boundary, so an exon that moves both of its boundaries is reported as both an a5ss and an a3ss.
• Added get_seq() to extract exon sequences from a GRanges against a genome.
• Results now carry event_type, event_tx_id and event_estimate, and any columns registered via additional_columns are propagated to the partner transcript with an event_ prefix.
  • Added long-form aliases for every finder (find_skipped_exons(), find_included_exons(), find_mutually_exclusive_exons(), find_retained_introns(), find_alternative_5_prime_splice_sites(), find_alternative_3_prime_splice_sites(), find_alternative_transcription_start_sites(), find_alternative_transcription_end_sites()).

splicelogic 0.99.0

Submit to Bioconductor 3.23