DifferentialRegulation

DOI: 10.18129/B9.bioc.DifferentialRegulation  

Differentially regulated genes from scRNA-seq data

Bioconductor version: Release (3.17)

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. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) 'ambiguous' reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).

Author: Simone Tiberi [aut, cre] , Charlotte Soneson [aut]

Maintainer: Simone Tiberi <simone.tiberi at unibo.it>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	DifferentialRegulation
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneTarget, Genetics, MultipleComparison, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Visualization
Version	1.4.2
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3
Depends	R (>= 4.3.0)
Imports	methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2, tximport
LinkingTo	Rcpp, RcppArmadillo
Suggests	knitr, rmarkdown, testthat, BiocStyle
SystemRequirements	C++11
Enhances
URL	https://github.com/SimoneTiberi/DifferentialRegulation
BugReports	https://github.com/SimoneTiberi/DifferentialRegulation/issues
Depends On Me
Imports Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DifferentialRegulation_1.4.2.tar.gz
Windows Binary	DifferentialRegulation_1.4.2.zip
macOS Binary (x86_64)	DifferentialRegulation_1.4.2.tgz
macOS Binary (arm64)	DifferentialRegulation_1.4.2.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 3.17	Source Archive