BANDITS
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BANDITS.
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Bioconductor version: 3.9
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("BANDITS")):
Installation
To install this package, start R (version "3.6") 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")| 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, Transcription, WorkflowStep |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.6.0) |
| Imports | Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel |
| System Requirements | C++11 |
| 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 | |
| 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_1.0.0.tar.gz |
| Windows Binary | BANDITS_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | BANDITS_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BANDITS |
| Source Repository (Developer Access) | git clone [email protected]:packages/BANDITS |
| Bioc Package Browser | https://code.bioconductor.org/browse/BANDITS/ |
| Package Short Url | https://bioconductor.org/packages/BANDITS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |