Changelog

Source: NEWS.md

splicelogic 1.2.0

• New event types: alternative transcription start and end sites (find_atss(), find_ates()) and spliced introns (find_si()).
• New input option: prepare_exons_by_partition() builds the input from two user-defined sets of transcripts (up and down). Unlike prepare_exons(), it does not need DTU results.
• get_seq() extracts exon sequences against a genome.
• Plotting functions for event results: plot_transcripts(), plot_transcripts_by_gene(), plot_transcripts_by_pair(), plot_transcript_lfc() and event_palette().
• Long-form aliases for every finder, e.g. find_skipped_exons().
• find_se(), find_ie(), find_mxe() and find_all_events() pass extra arguments on to GenomicRanges::findOverlaps().
• Results carry event_type, event_tx_id, event_estimate and event_<col> for any additional_columns.
• The default type is now "over"; "boundary" matches only the splice site facing the candidate; and "in" is renamed "identical".

splicelogic 1.1.5

• Added plotting functions for event results: plot_transcripts(), plot_transcripts_by_gene(), plot_transcripts_by_pair(), plot_transcript_lfc() and event_palette() (require ggplot2).
• Added find_si() for spliced introns, the reverse of find_ri().
• The default type of find_se(), find_ie(), find_mxe() and find_all_events() is now "over" (was "boundary").
• type = "boundary" now matches only the splice site of each flanking exon that faces the candidate exon, on either strand.
• The "in" match type is renamed "identical".
• find_se(), find_ie(), find_mxe() and find_all_events() pass extra arguments on to GenomicRanges::findOverlaps(), e.g. minoverlap = 5L.
• plyranges moved to Depends, so it is attached with splicelogic.

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.
• The default type of find_se(), find_ie(), find_mxe() and find_all_events() is now "over". "boundary" now requires the flank to share its inner boundary — the splice site facing the candidate — rather than either its start or its end, and is strand-aware. The "in" match type is renamed "identical". Extra arguments (...) are passed on to GenomicRanges::findOverlaps() when matching flanking exons.
• 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