BANDITS
This is the development version of BANDITS; for the stable release version, see BANDITS.
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, Genetics, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, Transcription, Visualization |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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_1.29.0.tar.gz |
| Windows Binary (x86_64) | BANDITS_1.29.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | BANDITS_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | BANDITS_1.29.0.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 |