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