Skip to contents

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 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.

Funding

splicelogic is supported by NHGRI R01-HG009937, and the Wellcome Trust as part of the EOSS program.