DifferentialRegulation
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see DifferentialRegulation.
Differentially regulated genes from scRNA-seq data
Bioconductor version: 3.16
DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. In particular, when reads are compatible with multiple genes or multiple splicing versions of a gene (unspliced spliced or ambiguous), the method allocates these multi-mapping reads to the gene of origin and their splicing version. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).
Author: Simone Tiberi [aut, cre] 
Maintainer: Simone Tiberi <simone.tiberi at uzh.ch>
citation("DifferentialRegulation")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DifferentialRegulation")
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("DifferentialRegulation")| DifferentialRegulation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneTarget, Genetics, MultipleComparison, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Visualization |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2 |
| System Requirements | C++11 |
| URL | https://github.com/SimoneTiberi/DifferentialRegulation |
| Bug Reports | https://github.com/SimoneTiberi/DifferentialRegulation/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle |
| 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 | DifferentialRegulation_1.2.2.tar.gz |
| Windows Binary | DifferentialRegulation_1.2.2.zip (64-bit only) |
| macOS Binary (x86_64) | DifferentialRegulation_1.2.2.tgz |
| macOS Binary (arm64) | DifferentialRegulation_1.2.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DifferentialRegulation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DifferentialRegulation |
| Bioc Package Browser | https://code.bioconductor.org/browse/DifferentialRegulation/ |
| Package Short Url | https://bioconductor.org/packages/DifferentialRegulation/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |