PROFILE INTERNSHIP (start 2021) - R package development of the shrinkISO method

Abstract

By varying the location of splice sites, a single gene can produce different transcripts. This alternative splicing leads to the production of different protein variants. Genomic differences between groups can lead to differential exon usage (DEU): a difference in the distribution of exon counts from the same gene. The shrinkISO method was developed to find DEU using an empirical Bayesian approach, mixed model methodology and integrated nested Laplacian approximation to test for DEU at the gene-level. The aim of this project was to develop an R package for this method. Prior to the development of the package, the method was used in the differential exon usage analysis of chromosome 22. Results of this analysis were used in the development of the package manual. The package improves the replicability as well as the usability of the method. The package will form a starting point for a detailed paper on the shrinkISO method.