BANDITS

DOI: 10.18129/B9.bioc.BANDITS    

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Bioconductor version: Release (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")

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
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Details

biocViews AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, Transcription, Visualization
Version 1.4.1
In Bioconductor since BioC 3.9 (R-3.6) (1.5 years)
License GPL (>= 3)
Depends R (>= 4.0.0)
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++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_1.4.1.tar.gz
Windows Binary BANDITS_1.4.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) BANDITS_1.4.1.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive

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