Ducasse is an R package that detects alternatively- spliced events from a transcriptome annotation file (GTF) and classifies them into the major splicing categories (Casette Exons [CE], Alternative Donor [AD], Alternative Acceptor [AA], Alternative First Exon [AF], Alternative Last Exon [AL] and Retained Intron [RI]). This tool outputs exon coordinates of all alternatively- spliced events as well as the intron coordinates that splices or skips the spliced events. The latter data facilitates the quantification of exon inclusion levels using the Percent-Spliced In (PSI) method.
The development version can be installed using devtools:
# install.packages("devtools")
devtools::install_github("f-hamidlab/Ducasse")The easiest way to use Ducasse is to supply the path to a GTF transcriptome
file to the findASevents function:
output <- Ducasse::findASevents("path/to/gtf")