BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty

Genome Biology

Mark D. Robinson¹  Simone Tiberi¹ 

[1] Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich;

关键词: Alternative splicing;    Differential splicing;    Differential transcript usage;    RNA-seq;    Transcriptomics;    Bayesian hierarchical modelling;   

DOI  :  10.1186/s13059-020-01967-8

来源: DOAJ

【 摘 要 】

Abstract 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.

【 授权许可】

Unknown