Shell scripts are:
01_star_fusion.sh (main run script to run fusion on all smart-seq2 fastqs)
01alt_joint_scstar_fusion.sh (test script, not used, to jointly run star-fusion)
02_get_genefusion_counts.sh (aggregate the fusion outputs)

Scripts for loading data in R:
load_fusion_data.R (load processed fusions)
load_go_signatures.R (expression signature data)
load_joint_expression.R (expression data)

Of the fusion analysis scripts (gene_fusions_*.R), the most relevant are:
gene_fusions_01_filter_fusions.R (filtering fusions)
gene_fusions_02_join_fusions_metadata.R (joining with metadata)
gene_fusions_04_regressions.R (regressions for Figure 1B)
gene_fusions_04c_compare_regressions_review.R (comparison of regression models for reviews)
gene_fusions_05_regressions_by_type.R (regression splitting fusions different ways)
gene_fusions_06_stratify_cells.R (gene signatures)
gene_fusions_06c_stratify_by_type.R (gene signatures by cell type)
gene_fusions_06d_gene_diff.R (DEGs associated with fusions, not in manuscript but available)

Other R scripts:
auxiliary_fusion_plotting.R (functions to facilitate fusion plotting)
statistics_qc_01_markers_ncounts.R (statistics on the smart-seq data for Figure S1)