BANDITS
This is thereleased version of BANDITS; for the devel version, seeBANDITS.
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Bioconductor version: Release (3.22)
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 unibo.it>
citation("BANDITS")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("BANDITS")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing,Bayesian,DifferentialExpression,DifferentialSplicing,GeneExpression,Genetics,MultipleComparison,RNASeq,Sequencing,Software,StatisticalMethod,Transcription,Visualization |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (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
FollowInstallation instructions to use this package in your R session.
| Source Package | BANDITS_1.26.0.tar.gz |
| Windows Binary (x86_64) | BANDITS_1.26.0.zip (64-bit only) |
| macOS Binary (x86_64) | BANDITS_1.26.0.tgz |
| macOS Binary (arm64) | BANDITS_1.26.0.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 |