Journal
GENOME BIOLOGY
Volume 21, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-020-01967-8
Keywords
Alternative splicing; Differential splicing; Differential transcript usage; RNA-seq; Transcriptomics; Bayesian hierarchical modelling; Markov chain Monte Carlo
Funding
- Swiss National Science Foundation [310030_175841, CRSII5_177208]
- Chan Zuckerberg Initiative DAF, Silicon Valley Community Foundation [2018-182828]
- University Research Priority Program Evolution in Action at the University of Zurich
- Swiss National Science Foundation (SNF) [CRSII5_177208, 310030_175841] Funding Source: Swiss National Science Foundation (SNF)
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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.
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