Package: BANDITS
Type: Package
Title: BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Version: 1.23.0
Author: Simone Tiberi [aut, cre].
Maintainer: Simone Tiberi <simone.tiberi@uzh.ch>
Description: 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.
biocViews: DifferentialSplicing, AlternativeSplicing, Bayesian, Genetics,
  RNASeq, Sequencing, DifferentialExpression, GeneExpression, MultipleComparison,
  Software, Transcription, StatisticalMethod, Visualization
License: GPL (>= 3)
Depends: R (>= 4.3.0)
Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2,
  DRIMSeq, BiocParallel
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, testthat,
  tximport, BiocStyle, GenomicFeatures, Biostrings
SystemRequirements: C++17
VignetteBuilder: knitr
RoxygenNote: 7.2.3
ByteCompile: true
URL: https://github.com/SimoneTiberi/BANDITS
BugReports: https://github.com/SimoneTiberi/BANDITS/issues