BANDITS

DOI: 10.18129/B9.bioc.BANDITS    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BANDITS.

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, Transcription, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 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	DifferentialRegulation
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BANDITS_1.12.0.tar.gz
Windows Binary	BANDITS_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	BANDITS_1.12.0.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/
Package Downloads Report	Download Stats