BANDITS

DOI: 10.18129/B9.bioc.BANDITS    

This is the development version of BANDITS; for the stable release version, see BANDITS.

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Bioconductor version: Development (3.11)

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 uzh.ch>

Citation (from within R, enter citation("BANDITS")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BANDITS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BANDITS")

 

HTML R Script BANDITS: Bayesian ANalysis of DIfferenTial Splicing
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, MultipleComparison, RNASeq, Sequencing, Software, Transcription, WorkflowStep
Version 1.3.0
In Bioconductor since BioC 3.9 (R-3.6) (0.5 years)
License GPL (>= 3)
Depends R (>= 3.6.0)
Imports Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel
LinkingTo Rcpp, RcppArmadillo
Suggests knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings
SystemRequirements C++11
Enhances
URL https://github.com/SimoneTiberi/BANDITS
BugReports https://github.com/SimoneTiberi/BANDITS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BANDITS_1.3.0.tar.gz
Windows Binary BANDITS_1.3.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) BANDITS_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BANDITS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BANDITS
Package Short Url https://bioconductor.org/packages/BANDITS/
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