Supporting code for figures in our 2025 Splicing Heuristics Manuscript (Sullivan et al.), "Data-driven insights to inform splice-altering variant assessment."
This repository provides the code and processing pipelines used to generate the figures and analyses for the manuscript. The primary goal of this project is to explore and assess splice-altering variant effects using data-driven heuristics. The variant data referenced in this repository can be linked to IDs in SpliceVarDB, though explicit variant information is not provided here.
The repository is organized into several directories, each with a specific role in the analysis pipeline:
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requirements/Includes the scripts to compute splicing requirements and create sequence logos. -
heuristics/Contains per-variant results for data-driven heuristics and plot code for spliceogenicity. -
novel/Contains the code to plot for pseudoexon inclusion mechanisms. -
outcomes/Code to plot the splicing transcript outcomes based on the location of the splice-altering variant. -
references/Holds the reference files.