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DifferentialRegulation
This is the released version of DifferentialRegulation; for the devel version, see DifferentialRegulation.
Differentially regulated genes from scRNA-seq data
Bioconductor version: Release (3.22)
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] ORCID iD ORCID: 0000-0002-3054-9964 , Charlotte Soneson [aut] ORCID iD ORCID: 0000-0003-3833-2169
Maintainer: Simone Tiberi <simone.tiberi at unibo.it>
citation("DifferentialRegulation")):
Installation
To install this package, start R (version "4.5") 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")
Details
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Follow Installation instructions to use this package in your R session.