DOI: 10.18129/B9.bioc.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>

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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) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2
LinkingTo Rcpp, RcppArmadillo
Suggests knitr, rmarkdown, testthat, BiocStyle
SystemRequirements C++11
URL https://github.com/SimoneTiberi/DifferentialRegulation
BugReports https://github.com/SimoneTiberi/DifferentialRegulation/issues
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