Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.
Genome Biol. 2020 Mar 16;21(1):69. doi: 10.1186/s13059-020-01967-8.
Alternative splicing is a biological process during gene expression that allows a single gene to code for multiple proteins. However, splicing patterns can be altered in some conditions or diseases. Here, we present BANDITS, a R/Bioconductor package to perform differential splicing, at both gene and transcript level, based on RNA-seq data. BANDITS uses a Bayesian hierarchical structure to explicitly model the variability between samples and treats the transcript allocation of reads as latent variables. We perform an extensive benchmark across both simulated and experimental RNA-seq datasets, where BANDITS has extremely favourable performance with respect to the competitors considered.
可变剪接是基因表达过程中的一种生物学过程，它允许一个基因编码多个蛋白质。然而，在某些情况下或疾病中，剪接模式可能会发生改变。在这里，我们提出了 BANDITS，这是一个基于 RNA-seq 数据进行差异剪接（在基因和转录本水平上）的 R/Bioconductor 包。BANDITS 使用贝叶斯层次结构来明确地对样本之间的变异性进行建模，并将读取的转录本分配视为潜在变量。我们在模拟和实验 RNA-seq 数据集上进行了广泛的基准测试，结果表明，BANDITS 在考虑的竞争对手中具有极好的性能。
