Truth table

The project contains the true differential state of each gene and transcript, as well as the simulation details, from simulated RNA-seq data for 12 paired-ended samples (i.e., biological replicates).
Column 'gene_ds_status' is 1 for differentially spliced genes, 0 otherwise.
Column 'gene_ds_status' is 1 for differentially expressed genes, 0 otherwise.Column 'transcript_ds_status' is 1 for differentially spliced transcripts, 0 otherwise.
With differentially splicing, we refer to differential transcript usage (DTU).

Samples belong to two groups: samples 1 to 6 constitute the first group, while samples 7 to 12 represent the second group.In each group 1,000 genes exhibit differential transcript usage (DTU) and further 1,000 genes (partially overlapping with the previous set) shows differential gene expression (DGE) between groups.
Genes showing DTU were simulated by randomly permuting the relative abundance of the four most expressed transcripts; for gene with two or three transcripts only, all transcripts relative abundances were permuted.
The dataset is used to benchmark DTU methods in the manuscript entitled "BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty".
The code for simulating the data is available on GitHub at https://github.com/SimoneTiberi/BANDITS_manuscript .