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 6contains the code to simulate the "6 vs 6" data used in the paper. The simulated RNA-seq reads are available at FigShare (https://figshare.com/projects/RNA-seq_simulated_data_for_differential_transcript_usage_DTU_analyses/66275) with DOI
Alignment and quantificationcontains the code to align and quantify reads.
Methodscontains the code to run all differential splicing methods.
Plots and Tablescontains the code to make all Figures and Tables available in the manuscript and its Supplementary.