DOI: 10.18129/B9.bioc.BANDITS    

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BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Bioconductor version: Development (3.10)

BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.

Author: Simone Tiberi [aut, cre], Mark D. Robinson [aut].

Maintainer: Simone Tiberi <simone.tiberi at>

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biocViews AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, MultipleComparison, RNASeq, Sequencing, Software, Transcription, WorkflowStep
Version 1.1.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL (>= 3)
Depends R (>= 3.6.0)
Imports Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel
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Suggests knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings
SystemRequirements C++11
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