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Differentially regulated genes from scRNA-seq data

Bioconductor version: Release (3.18)

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")):


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Reference Manual PDF


biocViews Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneTarget, Genetics, MultipleComparison, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Visualization
Version 2.0.3
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
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Suggests knitr, rmarkdown, testthat, BiocStyle
Linking To Rcpp, RcppArmadillo
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Source Package DifferentialRegulation_2.0.3.tar.gz
Windows Binary DifferentialRegulation_2.0.3.zip
macOS Binary (x86_64) DifferentialRegulation_2.0.3.tgz
macOS Binary (arm64) DifferentialRegulation_2.0.3.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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