BANDITS

DOI:10.18129/B9.bioc.BANDITS

This is thedevelopmentversion of BANDITS; for the stable release version, seeBANDITS.

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Bioconductor version: Development (3.16)

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

Installation

To install this package, start R (version "4.2") 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 appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.13.0
In Bioconductor since	BioC 3.9 (R-3.6) (3 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

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	BANDITS_1.13.0.tar.gz
Windows Binary	BANDITS_1.13.0.zip(64-bit only)
macOS 10.13 (High Sierra)	BANDITS_1.13.0.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	//www.andersvercelli.com/packages/BANDITS/
Package Downloads Report	Download Stats