Alternative splicing contributes to the diversity of RNA found in biological samples.
Current tools investigating patterns of alternative splicing check for coordinated
changes in the expression or relative ratio of RNA isoforms where specific isoforms
are up- or downregulated in a condition. However, the molecular process of splicing
is stochastic and changes in RNA isoform diversity for a gene might arise between
samples or conditions. A specific condition can be dominated by a single isoform,
while multiple isoforms with similar expression levels can be present in a different
condition. These changes might be the result of mutations, drug treatments or differences
in the cellular or tissue environment. Here, we present a tool for the characterization
and analysis of RNA isoform diversity using isoform level expression measurements.We
developed an R package called SplicingFactory, to calculate various RNA isoform diversity
metrics, and compare them across conditions. Using the package, we tested the effect
of RNA-seq quantification tools, quantification uncertainty, gene expression levels,
and isoform numbers on the isoform diversity calculation. We analyzed a set of CD34+
hematopoietic stem cells and myelodysplastic syndrome samples and found a set of genes
whose isoform diversity change is associated with SF3B1 mutations.The SplicingFactory
package is freely available under the GPL-3.0 license from Bioconductor for the Windows,
MacOS and Linux operating systems (https://www.bioconductor.org/packages/release/bioc/html/SplicingFactory.html).Supplementary
data are available at Bioinformatics online.
