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DifferentialRegulation

This is the development version of DifferentialRegulation; for the stable release version, see DifferentialRegulation.

Differentially regulated genes from scRNA-seq data


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("DifferentialRegulation")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneTarget, Genetics, MultipleComparison, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Visualization
Version 2.1.3
In Bioconductor since BioC 3.15 (R-4.2) (2 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, gridExtra
System Requirements C++17
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
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Package Archives

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

Source Package DifferentialRegulation_2.1.3.tar.gz
Windows Binary DifferentialRegulation_2.1.3.zip (64-bit only)
macOS Binary (x86_64) DifferentialRegulation_2.1.3.tgz
macOS Binary (arm64) DifferentialRegulation_2.1.3.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/
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