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BANDITS

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

BANDITS: Bayesian ANalysis of DIfferenTial Splicing


Bioconductor version: Development (3.19)

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].

Maintainer: Simone Tiberi <simone.tiberi at uzh.ch>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")
BANDITS: Bayesian ANalysis of DIfferenTial Splicing HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, Transcription, Visualization
Version 1.19.1
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
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
System Requirements C++17
URL https://github.com/SimoneTiberi/BANDITS
Bug Reports https://github.com/SimoneTiberi/BANDITS/issues
See More
Suggests knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings
Linking To Rcpp, RcppArmadillo
Enhances
Depends On Me
Imports Me DifferentialRegulation
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package BANDITS_1.19.1.tar.gz
Windows Binary BANDITS_1.19.1.zip (64-bit only)
macOS Binary (x86_64) BANDITS_1.19.1.tgz
macOS Binary (arm64) BANDITS_1.19.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/BANDITS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BANDITS
Bioc Package Browser https://code.bioconductor.org/browse/BANDITS/
Package Short Url https://bioconductor.org/packages/BANDITS/
Package Downloads Report Download Stats