This repository contains the code used for the analyses presented in the manuscript "BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty", which presents the differential splicing R/Bioconductor package BANDITS.

The code is organized in four folders:

• Simulated data 6 vs 6 contains the code to simulate the "6 vs 6" data used in the paper. The simulated RNA-seq reads are available at FigShare, with DOI 10.6084/m9.figshare.9467144, 10.6084/m9.figshare.9692429 and 10.6084/m9.figshare.9692918.

• Alignment and quantification contains the code to align and quantify reads.

• Methods contains the code to run all differential splicing methods.

• Plots and Tables contains the code to make all Figures and Tables available in the manuscript and its Supplementary.