MAJIQ analysis conducted using script src/majiq.sh. To produce correct GFF format, this script additionally calls src/add_gene_names.awk.

After MAJIQ has run, results are analyzed (and figures created) with R/deltapsi.R.

Script R/format_literature.R was used to compile the list of DAS genes used in the main script.

Other, more exploratory scripts are stored in separate branch exploratory, including VOILA modulizer separately ran with src/modulize.sh (not included in paper).