# splicelogic: DTU to splice events _splicelogic_ allows users to find alternative splicing events after performing differential transcript usage (DTU) analysis. Unlike event-based tools that work at the junction level, _splicelogic_ operates on whole transcript structures: each transcript and all its exons are annotated with a DTU effect estimate, allowing splicing events to be derived directly from transcript quantification with full isoform context. By comparing up- and down-regulated transcripts, _splicelogic_ can detect skipped exons, included exons, mutually exclusive exons, retained introns, and alternative 5' and 3'splice sites. Because it takes transcript-level effect estimates as input, it is compatible with any upstream DTU method (including DRIMSeq, DEXSeq, satuRn, and edgeR), supporting flexible experimental designs. *splicelogic* operates on exon-level data stored as *GRanges* objects within R/Bioconductor. Given a set of exons annotated with a coefficient column indicating differential transcript usage (DTU), _splicelogic_ can be used to identify a variety of splicing events. See the [vignette](https://thelovelab.github.io/splicelogic/articles/splicelogic.html) for more details. # How to install `splicelogic` will be submitted to Bioconductor. For now you can test it by installing from GitHub: ``` devtools::install_github("thelovelab/splicelogic") ``` # Quick start ``` # prepare exons from a TxDb and DTU results exons <- prepare_exons( txdb = <A TxDb OBJECT>, dtu_table = <DTU_TABLE>, coef_col = "estimate" ) # preprocess for further analysis exons <- preprocess(exons, coef_col = "estimate") # find skipped exons skipped <- exons |> find_se() # find all splicing events all_events <- exons |> find_all_events() ``` # Future directions - Support detection of alternative UTR events (alternative 5' and 3' UTRs), when the reference annotation includes UTR coordinates (e.g. GENCODE). - Support detection of additional event types, such as consecutive skipped exons or loss of retained introns. - Extraction and labelling of the specific splice junctions associated with each event, adding metadata columns such as the donor–acceptor dinucleotide sequence (e.g. AG-GT) and a logical indicating whether the junction is canonical, for downstream interpretation. - Facilitating RNA-binding protein (RBP) motif detection. - Facilitating interpretation of downstream structural consequences. # Feedback We would love to hear your feedback. Please post to an [Issue on GitHub](https://github.com/thelovelab/splicelogic/issues/new). # Funding _splicelogic_ is supported by NHGRI R01-HG009937, and the Wellcome Trust as part of the EOSS program.